{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T18:58:10Z","timestamp":1766084290709,"version":"3.48.0"},"reference-count":293,"publisher":"Elsevier","isbn-type":[{"type":"print","value":"9780443429590"}],"license":[{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/100013003","name":"University of Cagliari","doi-asserted-by":"publisher","award":["ECS00000038"],"award-info":[{"award-number":["ECS00000038"]}],"id":[{"id":"10.13039\/100013003","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013003","name":"University of Cagliari","doi-asserted-by":"publisher","award":["F53C22000430001"],"award-info":[{"award-number":["F53C22000430001"]}],"id":[{"id":"10.13039\/100013003","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013003","name":"University of Cagliari","doi-asserted-by":"publisher","award":["PE00000019"],"award-info":[{"award-number":["PE00000019"]}],"id":[{"id":"10.13039\/100013003","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021856","name":"Ministero dell&apos;Universit\u00e0 e della Ricerca","doi-asserted-by":"publisher","award":["PE00000007"],"award-info":[{"award-number":["PE00000007"]}],"id":[{"id":"10.13039\/501100021856","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021856","name":"Ministero dell&apos;Universit\u00e0 e della Ricerca","doi-asserted-by":"publisher","award":["F53C22000720007"],"award-info":[{"award-number":["F53C22000720007"]}],"id":[{"id":"10.13039\/501100021856","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025]]},"DOI":"10.1016\/bs.mie.2025.10.001","type":"book-chapter","created":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T13:59:49Z","timestamp":1762610389000},"page":"299-361","source":"Crossref","is-referenced-by-count":0,"title":["Computational approaches for modelling multidrug efflux pumps of the resistance nodulation-cell division superfamily"],"prefix":"10.1016","member":"78","reference":[{"issue":"7","key":"10.1016\/bs.mie.2025.10.001_bib1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0159154","article-title":"Structures of gate loop variants of the AcrB drug efflux pump bound by erythromycin substrate","volume":"11","author":"Ababou","year":"2016","journal-title":"PLoS One"},{"key":"10.1016\/bs.mie.2025.10.001_bib2","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"issue":"8016","key":"10.1016\/bs.mie.2025.10.001_bib3","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib4","doi-asserted-by":"crossref","DOI":"10.1002\/minf.202200188","article-title":"Speed vs accuracy: Effect on ligand pose accuracy of varying box size and exhaustiveness in AutoDock vina","volume":"42","author":"Agarwal","year":"2023","journal-title":"Molecular Informatics"},{"year":"2021","series-title":"Global antimicrobial resistance and use surveillance system (GLASS) report","author":"Agnew","key":"10.1016\/bs.mie.2025.10.001_bib5"},{"issue":"51","key":"10.1016\/bs.mie.2025.10.001_bib6","doi-asserted-by":"crossref","first-page":"52816","DOI":"10.1074\/jbc.C400445200","article-title":"Crystal structure of the drug discharge outer membrane protein, OprM, of pseudomonas aeruginosa - dual modes of membrane anchoring and occluded cavity end","volume":"279","author":"Akama","year":"2004","journal-title":"Journal of Biological Chemistry"},{"issue":"25","key":"10.1016\/bs.mie.2025.10.001_bib7","doi-asserted-by":"crossref","first-page":"25939","DOI":"10.1074\/jbc.C400164200","article-title":"Crystal structure of the membrane fusion protein, MexA, of the multidrug transporter in pseudomonas aeruginosa","volume":"279","author":"Akama","year":"2004","journal-title":"Journal of Biological Chemistry"},{"issue":"9","key":"10.1016\/bs.mie.2025.10.001_bib8","doi-asserted-by":"crossref","first-page":"5479","DOI":"10.1021\/acs.chemrev.1c00055","article-title":"Structure, assembly, and function of tripartite efflux and type 1 secretion systems in gram-negative bacteria","volume":"121","author":"Alav","year":"2021","journal-title":"Chemical Reviews"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib9","doi-asserted-by":"crossref","DOI":"10.1002\/adts.202100391","article-title":"Martini 3 coarse\u2010grained force field: Small molecules","volume":"5","author":"Alessandri","year":"2022","journal-title":"Advanced Theory and Simulations"},{"issue":"12","key":"10.1016\/bs.mie.2025.10.001_bib10","doi-asserted-by":"crossref","first-page":"1952","DOI":"10.1002\/jcc.21172","article-title":"GridMAT-MD: A grid-based membrane analysis tool for use with molecular dynamics","volume":"30","author":"Allen","year":"2009","journal-title":"Journal of Computational Chemistry"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib11","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"Journal of Molecular Biology"},{"key":"10.1016\/bs.mie.2025.10.001_bib12","doi-asserted-by":"crossref","first-page":"40475","DOI":"10.3389\/fmicb.2013.00007","article-title":"RND multidrug efflux pumps: What are they good for?","volume":"4","author":"Alvarez-Ortega","year":"2013","journal-title":"Frontiers in Microbiology"},{"issue":"4","key":"10.1016\/bs.mie.2025.10.001_bib13","doi-asserted-by":"crossref","DOI":"10.1038\/s41570-018-0148","article-title":"Multiscale methods in drug design bridge chemical and biological complexity in the search for cures","volume":"2","author":"Amaro","year":"2018","journal-title":"Nature Reviews Chemistry"},{"issue":"7-8","key":"10.1016\/bs.mie.2025.10.001_bib14","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1016\/j.resmic.2017.11.001","article-title":"The hydrophobic trap\u2014the achilles heel of RND efflux pumps","volume":"169","author":"Aron","year":"2018","journal-title":"Research in Microbiology"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib15","doi-asserted-by":"crossref","DOI":"10.1099\/mic.0.001307","article-title":"Tripartite efflux pumps of the RND superfamily: What did we learn from computational studies?","volume":"169","author":"Athar","year":"2023","journal-title":"Microbiology (Reading, England)"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib16","doi-asserted-by":"crossref","first-page":"397a","DOI":"10.1016\/j.bpj.2023.11.2432","article-title":"Molecular rationale for the specificities of mex transporters of pseudomonas aeruginosa","volume":"123","author":"Athar","year":"2024","journal-title":"Biophysical Journal"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib17","doi-asserted-by":"crossref","first-page":"860","DOI":"10.3390\/ijms21030860","article-title":"Molecular interactions of carbapenem antibiotics with the multidrug efflux transporter AcrB of escherichia coli","volume":"21","author":"Atzori","year":"2020","journal-title":"International Journal of Molecular Sciences"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib18","doi-asserted-by":"crossref","first-page":"860","DOI":"10.3390\/ijms21030860","article-title":"Molecular interactions of carbapenem antibiotics with the multidrug efflux transporter AcrB of escherichia coli","volume":"21","author":"Atzori","year":"2020","journal-title":"International Journal of Molecular Sciences"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib19","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1016\/j.bbamem.2018.10.012","article-title":"Identification and characterization of carbapenem binding sites within the RND-transporter AcrB","volume":"1861","author":"Atzori","year":"2019","journal-title":"Biochimica et Biophysica Acta (BBA)-Biomembranes"},{"issue":"22","key":"10.1016\/bs.mie.2025.10.001_bib20","doi-asserted-by":"crossref","first-page":"4625","DOI":"10.1021\/acs.jpcb.9b01351","article-title":"Molecular interactions of cephalosporins with the deep binding pocket of the RND transporter AcrB","volume":"123","author":"Atzori","year":"2019","journal-title":"The Journal of Physical Chemistry. B"},{"key":"10.1016\/bs.mie.2025.10.001_bib21","doi-asserted-by":"crossref","unstructured":"Balabin I. A. (2010). Membrane Plug-in. 1.1 ed.","DOI":"10.1109\/POWERCON.2010.5666079"},{"key":"10.1016\/bs.mie.2025.10.001_bib22","doi-asserted-by":"crossref","DOI":"10.1021\/acs.jcim.4c01810","article-title":"Toward the prediction of binding events in very flexible, allosteric, multidomain proteins","author":"Basciu","year":"2025","journal-title":"Journal of Chemical Information and Modeling"},{"issue":"4","key":"10.1016\/bs.mie.2025.10.001_bib23","doi-asserted-by":"crossref","first-page":"1515","DOI":"10.1021\/acs.jcim.8b00730","article-title":"Holo-like and druggable protein conformations from enhanced sampling of binding pocket volume and shape","volume":"59","author":"Basciu","year":"2019","journal-title":"Journal of Chemical Information and Modeling"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib24","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1016\/j.molcel.2008.02.015","article-title":"Assembly and channel opening in a bacterial drug efflux machine","volume":"30","author":"Bavro","year":"2008","journal-title":"Molecular Cell"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib25","doi-asserted-by":"crossref","first-page":"2155","DOI":"10.1063\/1.462066","article-title":"Density\u2010functional thermochemistry. I. the effect of the exchange\u2010only gradient correction","volume":"96","author":"Becke","year":"1992","journal-title":"The Journal of Chemical Physics"},{"issue":"1-3","key":"10.1016\/bs.mie.2025.10.001_bib26","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/0010-4655(95)00042-E","article-title":"GROMACS: A message-passing parallel molecular dynamics implementation","volume":"91","author":"Berendsen","year":"1995","journal-title":"Computer Physics Communications"},{"issue":"4","key":"10.1016\/bs.mie.2025.10.001_bib27","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1004180","article-title":"Interaction of the antimicrobial peptide polymyxin B1 with both membranes of E. Coli: A molecular dynamics study","volume":"11","author":"Berglund","year":"2015","journal-title":"PLoS Computational Biology"},{"key":"10.1016\/bs.mie.2025.10.001_bib28","first-page":"3","article-title":"Atomistic force fields for proteins","author":"Best","year":"2019","journal-title":"Biomolecular Simulations: Methods and Protocols"},{"issue":"11","key":"10.1016\/bs.mie.2025.10.001_bib29","doi-asserted-by":"crossref","first-page":"3511","DOI":"10.1073\/pnas.1419939112","article-title":"AcrB drug-binding pocket substitution confers clinically relevant resistance and altered substrate specificity","volume":"112","author":"Blair","year":"2015","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"10","key":"10.1016\/bs.mie.2025.10.001_bib30","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.2217\/fmb.14.66","article-title":"Multidrug efflux pumps in Gram-negative bacteria and their role in antibiotic resistance","volume":"9","author":"Blair","year":"2014","journal-title":"Future Microbiology"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib31","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1038\/nrmicro3380","article-title":"Molecular mechanisms of antibiotic resistance","volume":"13","author":"Blair","year":"2015","journal-title":"Nature Reviews. Microbiology"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib32","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1021\/j100785a001","article-title":"Van der waals volumes and radii","volume":"68","author":"Bondi","year":"1964","journal-title":"The Journal of Physical Chemistry"},{"issue":"11","key":"10.1016\/bs.mie.2025.10.001_bib33","doi-asserted-by":"crossref","first-page":"3251","DOI":"10.1021\/acs.jctc.3c00039","article-title":"Development and benchmarking of open force field 2.0. 0: The sage small molecule force field","volume":"19","author":"Boothroyd","year":"2023","journal-title":"Journal of Chemical Theory and Computation"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib34","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1186\/s13321-021-00548-6","article-title":"ProLIF: A library to encode molecular interactions as fingerprints","volume":"13","author":"Bouysset","year":"2021","journal-title":"Journal of Cheminformatics"},{"issue":"5","key":"10.1016\/bs.mie.2025.10.001_bib35","doi-asserted-by":"crossref","first-page":"1268","DOI":"10.1006\/jmbi.1997.0926","article-title":"Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool","volume":"267","author":"Bower","year":"1997","journal-title":"Journal of Molecular Biology"},{"key":"10.1016\/bs.mie.2025.10.001_bib36","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/S0065-3233(03)66004-3","article-title":"Free energy calculations and ligand binding","volume":"66","author":"Brandsdal","year":"2003","journal-title":"Advances in Protein Chemistry"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib37","article-title":"FATSLiM: A fast and robust software to analyze MD simulations of membranes","volume":"33","author":"Buchoux","year":"2017","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"21","key":"10.1016\/bs.mie.2025.10.001_bib38","doi-asserted-by":"crossref","first-page":"6469","DOI":"10.1021\/acs.jcim.3c01053","article-title":"SwissParam 2023: A modern web-based tool for efficient small molecule parametrization","volume":"63","author":"Bugnon","year":"2023","journal-title":"Journal of Chemical Information and Modeling"},{"issue":"8","key":"10.1016\/bs.mie.2025.10.001_bib39","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/s41429-023-00629-8","article-title":"Antibiotics in the clinical pipeline as of December 2022","volume":"76","author":"Butler","year":"2023","journal-title":"The Journal of Antibiotics"},{"key":"10.1016\/bs.mie.2025.10.001_bib40","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1016\/j.csbj.2021.11.042","article-title":"Molecular rationale for the impairment of the MexAB-OprM efflux pump by a single mutation in MexA","volume":"20","author":"Cacciotto","year":"2022","journal-title":"Computational and Structural Biotechnology Journal"},{"key":"10.1016\/bs.mie.2025.10.001_bib41","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1007\/978-1-4939-7454-2_11","article-title":"Molecular modeling of multidrug properties of resistance nodulation division (RND) transporters","volume":"1700","author":"Cacciotto","year":"2018","journal-title":"Bacterial Multidrug Exporters: Methods and Protocols"},{"key":"10.1016\/bs.mie.2025.10.001_bib42","doi-asserted-by":"crossref","first-page":"4538","DOI":"10.1016\/j.csbj.2021.08.011","article-title":"A review on machine learning approaches and trends in drug discovery","volume":"19","author":"Carracedo-Reboredo","year":"2021","journal-title":"Computational and structural biotechnology journal"},{"year":"2022","series-title":"Amber 2022","author":"Case","key":"10.1016\/bs.mie.2025.10.001_bib43"},{"key":"10.1016\/bs.mie.2025.10.001_bib44","doi-asserted-by":"crossref","DOI":"10.3389\/fphar.2022.1021916","article-title":"Common recognition topology of mex transporters of pseudomonas aeruginosa revealed by molecular modelling","volume":"13","author":"Catte","year":"2022","journal-title":"Frontiers in Pharmacology"},{"issue":"12","key":"10.1016\/bs.mie.2025.10.001_bib45","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1002\/bip.22331","article-title":"Twenty-five years of nucleic acid simulations","volume":"99","author":"Cheatham","year":"2013","journal-title":"Biopolymers"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib46","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.tips.2014.12.001","article-title":"Beware of docking!","volume":"36","author":"Chen","year":"2015","journal-title":"Trends in Pharmacological Sciences"},{"issue":"8","key":"10.1016\/bs.mie.2025.10.001_bib47","doi-asserted-by":"crossref","first-page":"1569","DOI":"10.1002\/jcc.21450","article-title":"Basic ingredients of free energy calculations: A review","volume":"31","author":"Christ","year":"2010","journal-title":"Journal of Computational Chemistry"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib48","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1007\/s00239-019-09914-3","article-title":"Antimicrobial resistance in bacteria: Mechanisms, evolution, and persistence","volume":"88","author":"Christaki","year":"2020","journal-title":"Journal of Molecular Evolution"},{"issue":"5","key":"10.1016\/bs.mie.2025.10.001_bib49","article-title":"Polarizable force field development for lipids and their efficient applications in membrane proteins","volume":"7","author":"Chu","year":"2017","journal-title":"Wiley Interdisciplinary Reviews: Computational Molecular Science"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib50","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1140\/epjb\/s10051-021-00249-x","article-title":"Molecular simulations: Past, present, and future (a Topical Issue in EPJB)","volume":"95","author":"Ciccotti","year":"2022","journal-title":"The European Physical Journal B"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib51","doi-asserted-by":"crossref","first-page":"143","DOI":"10.2217\/fmb-2019-0235","article-title":"RND efflux pumps in Gram-negative bacteria; regulation, structure and role in antibiotic resistance","volume":"15","author":"Colclough","year":"2020","journal-title":"Future Microbiology"},{"issue":"5","key":"10.1016\/bs.mie.2025.10.001_bib52","doi-asserted-by":"crossref","first-page":"2312","DOI":"10.1021\/acs.jctc.6b00027","article-title":"Biomolecular force field parameterization via atoms-in-molecule electron density partitioning","volume":"12","author":"Cole","year":"2016","journal-title":"Journal of Chemical Theory and Computation"},{"issue":"46","key":"10.1016\/bs.mie.2025.10.001_bib53","doi-asserted-by":"crossref","first-page":"19146","DOI":"10.1021\/ja307803m","article-title":"Recognition of imipenem and meropenem by the RND-Transporter MexB studied by computer simulations","volume":"134","author":"Collu","year":"2012","journal-title":"Journal of the American Chemical Society"},{"issue":"14","key":"10.1016\/bs.mie.2025.10.001_bib54","doi-asserted-by":"crossref","DOI":"10.1063\/1.2829861","article-title":"Adaptive biasing force method for scalar and vector free energy calculations","volume":"128","author":"Darve","year":"2008","journal-title":"The Journal of Chemical Physics"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib55","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1016\/j.jsb.2006.12.004","article-title":"Crystal structure of the multidrug efflux transporter AcrB at 3.1 \u00e5 resolution reveals the N-terminal region with conserved amino acids","volume":"158","author":"Das","year":"2007","journal-title":"Journal of Structural Biology"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib56","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1007\/s10822-018-0111-4","article-title":"Biomolecular force fields: Where have we been, where are we now, where do we need to go and how do we get there?","volume":"33","author":"Dauber-Osguthorpe","year":"2019","journal-title":"J Comput-Aided Mol Des"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib57","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms10731","article-title":"Tripartite assembly of RND multidrug efflux pumps","volume":"7","author":"Daury","year":"2016","journal-title":"Nature communications"},{"issue":"9","key":"10.1016\/bs.mie.2025.10.001_bib58","doi-asserted-by":"crossref","first-page":"4035","DOI":"10.1021\/acs.jmedchem.5b01684","article-title":"Role of molecular dynamics and related methods in drug discovery","volume":"59","author":"De Vivo","year":"2016","journal-title":"Journal of Medicinal Chemistry"},{"issue":"37","key":"10.1016\/bs.mie.2025.10.001_bib59","doi-asserted-by":"crossref","first-page":"9617","DOI":"10.1039\/c2sm26007g","article-title":"GAFFlipid: A general amber force field for the accurate molecular dynamics simulation of phospholipid","volume":"8","author":"Dickson","year":"2012","journal-title":"Soft Matter"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib60","doi-asserted-by":"crossref","first-page":"1726","DOI":"10.1021\/acs.jctc.1c01217","article-title":"Lipid21: Complex lipid membrane simulations with AMBER","volume":"18","author":"Dickson","year":"2022","journal-title":"Journal of Chemical Theory and Computation"},{"issue":"8","key":"10.1016\/bs.mie.2025.10.001_bib61","doi-asserted-by":"crossref","first-page":"1473","DOI":"10.1021\/acs.jcim.8b00261","article-title":"Steered molecular dynamics simulation in rational drug design","volume":"58","author":"Do","year":"2018","journal-title":"Journal of Chemical Information and Modeling"},{"key":"10.1016\/bs.mie.2025.10.001_bib62","doi-asserted-by":"crossref","first-page":"W665","DOI":"10.1093\/nar\/gkh381","article-title":"PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations","volume":"32","author":"Dolinsky","year":"2004","journal-title":"Nucleic Acids Research"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib63","doi-asserted-by":"crossref","first-page":"144","DOI":"10.3390\/ijms17020144","article-title":"Insights into protein\u2013ligand interactions: Mechanisms, models, and methods","volume":"17","author":"Du","year":"2016","journal-title":"International journal of molecular sciences"},{"issue":"6","key":"10.1016\/bs.mie.2025.10.001_bib64","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1016\/j.str.2020.03.013","article-title":"Interactions of a bacterial RND transporter with a transmembrane small protein in a lipid environment","volume":"28","author":"Du","year":"2020","journal-title":"Structure (London, England: 1993)"},{"issue":"5","key":"10.1016\/bs.mie.2025.10.001_bib65","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1016\/j.tim.2015.01.010","article-title":"Assembly and operation of bacterial tripartite multidrug efflux pumps","volume":"23","author":"Du","year":"2015","journal-title":"Trends in Microbiology"},{"issue":"7501","key":"10.1016\/bs.mie.2025.10.001_bib66","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1038\/nature13205","article-title":"Structure of the AcrAB-TolC multidrug efflux pump","volume":"509","author":"Du","year":"2014","journal-title":"Nature"},{"issue":"9","key":"10.1016\/bs.mie.2025.10.001_bib67","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/s41579-018-0048-6","article-title":"Multidrug efflux pumps: Structure, function and regulation","volume":"16","author":"Du","year":"2018","journal-title":"Nature Reviews. Microbiology"},{"issue":"8","key":"10.1016\/bs.mie.2025.10.001_bib68","doi-asserted-by":"crossref","first-page":"3891","DOI":"10.1021\/acs.jcim.1c00203","article-title":"AutoDock vina 1.2. 0: New docking methods, expanded force field, and python bindings","volume":"61","author":"Eberhardt","year":"2021","journal-title":"Journal of Chemical Information and Modeling"},{"issue":"15","key":"10.1016\/bs.mie.2025.10.001_bib69","doi-asserted-by":"crossref","first-page":"5687","DOI":"10.1073\/pnas.1114944109","article-title":"Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop","volume":"109","author":"Eicher","year":"2012","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"10.1016\/bs.mie.2025.10.001_bib70","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.03145","article-title":"Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB","volume":"3","author":"Eicher","year":"2014","journal-title":"elife"},{"issue":"23","key":"10.1016\/bs.mie.2025.10.001_bib71","doi-asserted-by":"crossref","first-page":"6490","DOI":"10.1128\/JB.184.23.6490-6499.2002","article-title":"Substrate specificity of the RND-Type multidrug efflux pumps AcrB and AcrD of escherichia coli is determined predominately by two large periplasmic loops","volume":"184","author":"Elkins","year":"2002","journal-title":"Journal of Bacteriology"},{"issue":"18","key":"10.1016\/bs.mie.2025.10.001_bib72","doi-asserted-by":"crossref","first-page":"5349","DOI":"10.1128\/JB.185.18.5349-5356.2003","article-title":"Chimeric analysis of AcrA function reveals the importance of its c-terminal domain in its interaction with the AcrB multidrug efflux pump","volume":"185","author":"Elkins","year":"2003","journal-title":"Journal of Bacteriology"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib73","doi-asserted-by":"crossref","first-page":"5.6.1","DOI":"10.1002\/0471250953.bi0506s15","article-title":"Comparative protein structure modeling using modeller","volume":"15","author":"Eswar","year":"2006","journal-title":"Current Protocols in Bioinformatics"},{"issue":"10","key":"10.1016\/bs.mie.2025.10.001_bib74","doi-asserted-by":"crossref","first-page":"1565","DOI":"10.1021\/ct800250m","article-title":"Replica-exchange accelerated molecular dynamics (REXAMD) applied to thermodynamic integration","volume":"4","author":"Fajer","year":"2008","journal-title":"Journal of Chemical Theory and Computation"},{"key":"10.1016\/bs.mie.2025.10.001_bib75","article-title":"Turning the juggernaut","volume":"6","author":"Fernandez","year":"2022"},{"issue":"9","key":"10.1016\/bs.mie.2025.10.001_bib76","doi-asserted-by":"crossref","first-page":"1753","DOI":"10.1110\/ps.9.9.1753","article-title":"Modeling of loops in protein structures","volume":"9","author":"Fiser","year":"2000","journal-title":"Protein Science"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib77","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/S0006-3495(03)74462-2","article-title":"Protocol for MM\/PBSA molecular dynamics simulations of proteins","volume":"85","author":"Fogolari","year":"2003","journal-title":"Biophysical Journal"},{"key":"10.1016\/bs.mie.2025.10.001_bib78","unstructured":"Frisch M. J., Trucks G. W., Schlegel H. B., Scuseria G. E., Robb M. A., Cheeseman J. R., & Fox D. J. (2016) Gaussian 16 Rev. A.03. Wallingford, CT."},{"key":"10.1016\/bs.mie.2025.10.001_bib79","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/j.ddtec.2021.08.001","article-title":"From computer-aided drug discovery to computer-driven drug discovery","volume":"39","author":"Frye","year":"2021","journal-title":"Drug Discovery Today: Technologies"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib80","doi-asserted-by":"crossref","DOI":"10.1002\/cpbi.108","article-title":"Protein sequence analysis using the MPI bioinformatics toolkit","volume":"72","author":"Gabler","year":"2020","journal-title":"Current Protocols in Bioinformatics"},{"key":"10.1016\/bs.mie.2025.10.001_bib81","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1007\/s10822-013-9684-0","article-title":"Computational analysis of local membrane properties","volume":"27","author":"Gapsys","year":"2013","journal-title":"Journal of Computer-Aided Molecular Design"},{"issue":"27","key":"10.1016\/bs.mie.2025.10.001_bib82","doi-asserted-by":"crossref","first-page":"16566","DOI":"10.1039\/D2CP00951J","article-title":"Recognition of quinolone antibiotics by the multidrug efflux transporter MexB of pseudomonas aeruginosa","volume":"24","author":"Gervasoni","year":"2022","journal-title":"Physical Chemistry Chemical Physics"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib83","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1038\/s41597-022-01261-1","article-title":"AB-DB: Force-field parameters, MD trajectories, QM-based data, and descriptors of antimicrobials","volume":"9","author":"Gervasoni","year":"2022","journal-title":"Scientific Data"},{"issue":"4","key":"10.1016\/bs.mie.2025.10.001_bib84","first-page":"e01403","article-title":"Molecular determinants of avoidance and inhibition of pseudomonas aeruginosa MexB efflux pump","volume":"14","author":"Gervasoni","year":"2023","journal-title":"Mbio"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib85","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1016\/S0006-3495(97)78756-3","article-title":"The statistical-thermodynamic basis for computation of binding affinities: A critical review","volume":"72","author":"Gilson","year":"1997","journal-title":"Biophysical Journal"},{"key":"10.1016\/bs.mie.2025.10.001_bib86","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1146\/annurev.biophys.36.040306.132550","article-title":"Calculation of protein-ligand binding affinities","volume":"36","author":"Gilson","year":"2007","journal-title":"Annual Review of Biophysics and Biomolecular Structure"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib87","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1038\/ng0393-266","article-title":"Identification of protein coding regions by database similarity search","volume":"3","author":"Gish","year":"1993","journal-title":"Nature Genetics"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib88","doi-asserted-by":"crossref","first-page":"4948","DOI":"10.1038\/s41467-020-18770-5","article-title":"Antibiotic export by MexB multidrug efflux transporter is allosterically controlled by a MexA-OprM chaperone-like complex","volume":"11","author":"Glavier","year":"2020","journal-title":"Nature Communications"},{"issue":"11","key":"10.1016\/bs.mie.2025.10.001_bib89","doi-asserted-by":"crossref","first-page":"2193","DOI":"10.1021\/acs.jcim.8b00639","article-title":"Molecular dynamics simulations of membrane proteins: An overview","volume":"58","author":"Goossens","year":"2018","journal-title":"Journal of Chemical Information and Modeling"},{"issue":"21","key":"10.1016\/bs.mie.2025.10.001_bib90","first-page":"2695","article-title":"Bio3d: An r package for the comparative analysis of protein structures","volume":"22","author":"Grant","year":"2006","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib91","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1002\/prot.21308","article-title":"Convergence of molecular dynamics simulations of membrane proteins","volume":"67","author":"Grossfield","year":"2007","journal-title":"Proteins"},{"key":"10.1016\/bs.mie.2025.10.001_bib92","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/S1574-1400(09)00502-7","article-title":"Quantifying uncertainty and sampling quality in biomolecular simulations","volume":"5","author":"Grossfield","year":"2009","journal-title":"Annual Reports in Computational Chemistry"},{"issue":"10","key":"10.1016\/bs.mie.2025.10.001_bib93","first-page":"1478","article-title":"MEMBPLUGIN: Studying membrane complexity in VMD","volume":"30","author":"Guixa-Gonzalez","year":"2014","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"7","key":"10.1016\/bs.mie.2025.10.001_bib94","doi-asserted-by":"crossref","first-page":"2632","DOI":"10.1021\/ct500161f","article-title":"Practical aspects of free-energy calculations: A review","volume":"10","author":"Hansen","year":"2014","journal-title":"Journal of Chemical Theory and Computation"},{"issue":"5","key":"10.1016\/bs.mie.2025.10.001_bib95","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1038\/nrm.2017.138","article-title":"Understanding the diversity of membrane lipid composition","volume":"19","author":"Harayama","year":"2018","journal-title":"Nature Reviews. Molecular Cell Biology"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib96","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1021\/jm0603365","article-title":"Comparison of shape-matching and docking as virtual screening tools","volume":"50","author":"Hawkins","year":"2007","journal-title":"Journal of Medicinal Chemistry"},{"key":"10.1016\/bs.mie.2025.10.001_bib97","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/j.sbi.2021.11.011","article-title":"Recent progress in general force fields of small molecules","volume":"72","author":"He","year":"2022","journal-title":"Current Opinion in Structural Biology"},{"issue":"27","key":"10.1016\/bs.mie.2025.10.001_bib98","doi-asserted-by":"crossref","first-page":"9994","DOI":"10.1073\/pnas.0400375101","article-title":"Structure of the periplasmic component of a bacterial drug efflux pump","volume":"101","author":"Higgins","year":"2004","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"67","key":"10.1016\/bs.mie.2025.10.001_bib99","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1146\/annurev-micro-092412-155718","article-title":"Structure and operation of bacterial tripartite pumps","volume":"67","author":"Hinchliffe","year":"2013","journal-title":"Annual Review of Microbiology"},{"issue":"41","key":"10.1016\/bs.mie.2025.10.001_bib100","doi-asserted-by":"crossref","first-page":"16696","DOI":"10.1073\/pnas.1210093109","article-title":"Conserved small protein associates with the multidrug efflux pump AcrB and differentially affects antibiotic resistance","volume":"109","author":"Hobbs","year":"2012","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"10.1016\/bs.mie.2025.10.001_bib101","doi-asserted-by":"crossref","first-page":"B864","DOI":"10.1103\/PhysRev.136.B864","article-title":"Inhomogeneous electron gas","volume":"136","author":"Hohenberg","year":"1964","journal-title":"Physical Review"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib102","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1021\/ci100275a","article-title":"Assessing the performance of the MM\/PBSA and MM\/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations","volume":"51","author":"Hou","year":"2010","journal-title":"Journal of Chemical Information and Modeling"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib103","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/nmeth.4067","article-title":"CHARMM36m: An improved force field for folded and intrinsically disordered proteins","volume":"14","author":"Huang","year":"2017","journal-title":"Nature Methods"},{"issue":"4","key":"10.1016\/bs.mie.2025.10.001_bib104","doi-asserted-by":"crossref","first-page":"520","DOI":"10.3390\/antibiotics11040520","article-title":"Bacterial multidrug efflux pumps at the frontline of antimicrobial resistance: an overview","volume":"11","author":"Huang","year":"2022","journal-title":"Antibiotics"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib105","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: Visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"Journal of Molecular Graphics"},{"key":"10.1016\/bs.mie.2025.10.001_bib106","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1007\/s10969-013-9154-x","article-title":"Crystal structure of AcrB complexed with linezolid at 3.5 \u00e5 resolution","volume":"14","author":"Hung","year":"2013","journal-title":"Journal of Structural and Functional Genomics"},{"key":"10.1016\/bs.mie.2025.10.001_bib107","article-title":"mCNN-GenEfflux: Enhanced predicting efflux protein and their super families by using generative proteins combined with multiple Windows convolution neural networks","author":"Hussain","year":"2025","journal-title":"QTJCB, Chemistry"},{"issue":"21","key":"10.1016\/bs.mie.2025.10.001_bib108","doi-asserted-by":"crossref","first-page":"3863","DOI":"10.1021\/jz501780a","article-title":"Building water models: A different approach","volume":"5","author":"Izadi","year":"2014","journal-title":"The Journal of Physical Chemistry Letters"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib109","first-page":"590","article-title":"Tripartite efflux pumps: Energy is required for dissociation, but not assembly or opening of the outer membrane channel of the pump","volume":"88","author":"Janganan","year":"2013","journal-title":"ARJMm"},{"issue":"17","key":"10.1016\/bs.mie.2025.10.001_bib110","doi-asserted-by":"crossref","first-page":"6290","DOI":"10.1073\/pnas.0711686105","article-title":"Calculation of protein-ligand binding free energy by using a polarizable potential","volume":"105","author":"Jiao","year":"2008","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"10.1016\/bs.mie.2025.10.001_bib111","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1146\/annurev-biophys-070317-033349","article-title":"Polarizable force fields for biomolecular simulations: Recent advances and applications","volume":"48","author":"Jing","year":"2019","journal-title":"Annual Review of Biophysics"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib112","doi-asserted-by":"crossref","first-page":"180","DOI":"10.14348\/molcells.2015.2277","article-title":"Structure of the tripartite multidrug efflux pump AcrAB-TolC suggests an alternative assembly mode","volume":"38","author":"Jin-Sik","year":"2015","journal-title":"Molecules and Cells"},{"issue":"11","key":"10.1016\/bs.mie.2025.10.001_bib113","doi-asserted-by":"crossref","first-page":"1859","DOI":"10.1002\/jcc.20945","article-title":"CHARMM-GUI: A web-based graphical user interface for CHARMM","volume":"29","author":"Jo","year":"2008","journal-title":"Journal of Computational Chemistry"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib114","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1021\/acs.jpcb.3c06602","article-title":"OPLS\/2020 force field for unsaturated hydrocarbons, alcohols, and ethers","volume":"128","author":"Jorgensen","year":"2023","journal-title":"The Journal of Physical Chemistry. B"},{"issue":"7873","key":"10.1016\/bs.mie.2025.10.001_bib115","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"10.1016\/bs.mie.2025.10.001_bib116","article-title":"Molecular simulations with a pretrained neural network and universal pairwise force fields","author":"Kabylda","year":"2025","journal-title":"ChemRxiv"},{"issue":"8-9","key":"10.1016\/bs.mie.2025.10.001_bib117","doi-asserted-by":"crossref","first-page":"1042","DOI":"10.1002\/ijch.201400074","article-title":"Significance of molecular dynamics simulations for life sciences","volume":"54","author":"Karplus","year":"2014","journal-title":"Israel Journal of Chemistry"},{"key":"10.1016\/bs.mie.2025.10.001_bib118","article-title":"Markov state models in drug design","volume":"67","author":"Keller","year":"2019","journal-title":"Biomolecular Simulations in Structure-based Drug Discovery"},{"key":"10.1016\/bs.mie.2025.10.001_bib119","doi-asserted-by":"crossref","DOI":"10.1016\/j.str.2023.09.012","article-title":"Computational microbiology of bacteria: Advancements in molecular dynamics simulations","author":"Khalid","year":"2023","journal-title":"Structure (London, England: 1993)"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib120","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1021\/acs.accounts.8b00377","article-title":"Atomistic and coarse grain simulations of the cell envelope of gram-negative bacteria: What have we learned?","volume":"52","author":"Khalid","year":"2018","journal-title":"Accounts of Chemical Research"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib121","doi-asserted-by":"crossref","DOI":"10.1099\/mic.0.001165","article-title":"What have molecular simulations contributed to understanding of Gram-negative bacterial cell envelopes?","volume":"168","author":"Khalid","year":"2022","journal-title":"Microbiology (Reading, England)"},{"issue":"40","key":"10.1016\/bs.mie.2025.10.001_bib122","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1021\/j100091a024","article-title":"Comparison of density-functional and Mp2 calculations on the water monomer and dimer","volume":"98","author":"Kim","year":"1994","journal-title":"Journal of Physical Chemistry A"},{"issue":"D1","key":"10.1016\/bs.mie.2025.10.001_bib123","doi-asserted-by":"crossref","first-page":"D1373","DOI":"10.1093\/nar\/gkac956","article-title":"PubChem 2023 update","volume":"51","author":"Kim","year":"2023","journal-title":"Nucleic Acids Research"},{"issue":"5","key":"10.1016\/bs.mie.2025.10.001_bib124","doi-asserted-by":"crossref","first-page":"1405","DOI":"10.1073\/pnas.1525143113","article-title":"Aminoacyl \u03b2-naphthylamides as substrates and modulators of AcrB multidrug efflux pump","volume":"113","author":"Kinana","year":"2016","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"46","key":"10.1016\/bs.mie.2025.10.001_bib125","doi-asserted-by":"crossref","first-page":"8342","DOI":"10.1021\/bi401303v","article-title":"Some ligands enhance the efflux of other ligands by the escherichia coli multidrug pump AcrB","volume":"52","author":"Kinana","year":"2013","journal-title":"Biochemistry"},{"key":"10.1016\/bs.mie.2025.10.001_bib126","doi-asserted-by":"crossref","DOI":"10.3389\/fmolb.2021.712085","article-title":"Recent developments in free energy calculations for drug discovery","volume":"8","author":"King","year":"2021","journal-title":"Frontiers in molecular biosciences"},{"issue":"5","key":"10.1016\/bs.mie.2025.10.001_bib127","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1063\/1.1749657","article-title":"Statistical mechanics of fluid mixtures","volume":"3","author":"Kirkwood","year":"1935","journal-title":"The Journal of Chemical Physics"},{"issue":"9","key":"10.1016\/bs.mie.2025.10.001_bib128","doi-asserted-by":"crossref","first-page":"5378","DOI":"10.1021\/acs.chemrev.0c00621","article-title":"Structural and functional diversity of resistance\u2013nodulation\u2013cell division transporters","volume":"121","author":"Klenotic","year":"2020","journal-title":"Chemical Reviews"},{"issue":"15","key":"10.1016\/bs.mie.2025.10.001_bib129","doi-asserted-by":"crossref","first-page":"10680","DOI":"10.1074\/jbc.M114.547794","article-title":"\u03b2-Lactam selectivity of multidrug transporters AcrB and AcrD resides in the proximal binding pocket","volume":"289","author":"Kobayashi","year":"2014","journal-title":"Journal of Biological Chemistry"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib130","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1111\/nyas.14239","article-title":"AcrB: A mean, keen, drug efflux machine","volume":"1459","author":"Kobylka","year":"2020","journal-title":"Annals of the New York Academy of Sciences"},{"key":"10.1016\/bs.mie.2025.10.001_bib131","doi-asserted-by":"crossref","first-page":"A1133","DOI":"10.1103\/PhysRev.140.A1133","article-title":"Self-Consistent equations including exchange and correlation effects","volume":"140","author":"Kohn","year":"1965","journal-title":"Physical Review"},{"issue":"12","key":"10.1016\/bs.mie.2025.10.001_bib132","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1021\/ar000033j","article-title":"Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models","volume":"33","author":"Kollman","year":"2000","journal-title":"Accounts of Chemical Research"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib133","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1007\/s10822-008-9238-z","article-title":"An improved method to predict the entropy term with the MM\/PBSA approach","volume":"23","author":"Kongsted","year":"2009","journal-title":"Journal of Computer-Aided Molecular Design"},{"issue":"6789","key":"10.1016\/bs.mie.2025.10.001_bib134","doi-asserted-by":"crossref","first-page":"914","DOI":"10.1038\/35016007","article-title":"Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export","volume":"405","author":"Koronakis","year":"2000","journal-title":"Nature"},{"issue":"5","key":"10.1016\/bs.mie.2025.10.001_bib135","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1038\/nprot.2015.043","article-title":"The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins","volume":"10","author":"Kozakov","year":"2015","journal-title":"Nature Protocols"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib136","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1128\/JB.01276-07","article-title":"Fitting periplasmic membrane fusion proteins to inner membrane transporters: Mutations that enable escherichia coli AcrA to function with pseudomonas aeruginosa MexB","volume":"190","author":"Krishnamoorthy","year":"2008","journal-title":"Journal of Bacteriology"},{"key":"10.1016\/bs.mie.2025.10.001_bib137","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1007\/s00232-010-9254-5","article-title":"Comparing membrane simulations to scattering experiments: Introducing the SIMtoEXP software","volume":"235","author":"Ku\u010derka","year":"2010","journal-title":"Journal of Membrane Biology"},{"issue":"W1","key":"10.1016\/bs.mie.2025.10.001_bib138","doi-asserted-by":"crossref","first-page":"W338","DOI":"10.1093\/nar\/gky356","article-title":"CABS-flex 2.0: A web server for fast simulations of flexibility of protein structures","volume":"46","author":"Kuriata","year":"2018","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/bs.mie.2025.10.001_bib139","doi-asserted-by":"crossref","first-page":"7300","DOI":"10.1021\/jp0143138","article-title":"D-RESP: Dynamically generated electrostatic potential derived charges from quantum mechanics \/ molecular mechanics simulations","author":"Laio","year":"2002","journal-title":"The Journal of Physical Chemistry B"},{"issue":"4","key":"10.1016\/bs.mie.2025.10.001_bib140","article-title":"Wielding the power of interactive molecular simulations","volume":"12","author":"Lanrezac","year":"2022","journal-title":"Wiley Interdisciplinary Reviews: Computational Molecular Science"},{"key":"10.1016\/bs.mie.2025.10.001_bib141","article-title":"Molecular basis for multidrug efflux by an anaerobic RND transporter","author":"Lawrence","year":"2025","journal-title":"bioRxiv"},{"issue":"9","key":"10.1016\/bs.mie.2025.10.001_bib142","doi-asserted-by":"crossref","first-page":"6227","DOI":"10.1021\/acs.chemrev.8b00384","article-title":"Developing and testing of lipid force fields with applications to modeling cellular membranes","volume":"119","author":"Leonard","year":"2019","journal-title":"Chemical Reviews"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib143","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1128\/CMR.00117-14","article-title":"The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria","volume":"28","author":"Li","year":"2015","journal-title":"Clinical Microbiology Reviews"},{"key":"10.1016\/bs.mie.2025.10.001_bib144","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1007\/978-1-0716-1394-8_13","article-title":"Preparing membrane proteins for simulation using CHARMM-GUI","volume":"2302","author":"Li","year":"2021","journal-title":"Methods in Molecular Biology"},{"issue":"12","key":"10.1016\/bs.mie.2025.10.001_bib145","first-page":"2801","article-title":"Comparison of nine programs predicting p k a values of pharmaceutical substances","volume":"49","author":"Liao","year":"2009","journal-title":"MCJJoci, Modeling"},{"key":"10.1016\/bs.mie.2025.10.001_bib146","first-page":"21","article-title":"Force fields for small molecules","volume":"2022","author":"Lin","year":"2019","journal-title":"Biomolecular simulations: Methods and Protocols"},{"issue":"D1","key":"10.1016\/bs.mie.2025.10.001_bib147","doi-asserted-by":"crossref","first-page":"D370","DOI":"10.1093\/nar\/gkr703","article-title":"OPM database and PPM web server: Resources for positioning of proteins in membranes","volume":"40","author":"Lomize","year":"2012","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/bs.mie.2025.10.001_bib148","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1007\/978-1-4939-1465-4_3","article-title":"Current status of protein force fields for molecular dynamics simulations","author":"Lopes","year":"2015","journal-title":"Molecular Modeling of Proteins"},{"issue":"13","key":"10.1016\/bs.mie.2025.10.001_bib149","doi-asserted-by":"crossref","first-page":"4299","DOI":"10.1021\/acs.jctc.3c00233","article-title":"Assessing the current state of amber force field modifications for DNA\u2500 2023 edition","volume":"19","author":"Love","year":"2023","journal-title":"Journal of Chemical Theory and Computation"},{"issue":"10","key":"10.1016\/bs.mie.2025.10.001_bib150","doi-asserted-by":"crossref","first-page":"2483","DOI":"10.1016\/j.bbamem.2015.12.033","article-title":"Force field development for lipid membrane simulations","volume":"1858","author":"Lyubartsev","year":"2016","journal-title":"Biochimica et Biophysica Acta (BBA)-Biomembranes"},{"key":"10.1016\/bs.mie.2025.10.001_bib151","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/S0076-6879(96)66011-X","article-title":"Applications of network BLAST server","volume":"266","author":"Madden","year":"1996","journal-title":"Methods in Enzymology"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib152","doi-asserted-by":"crossref","first-page":"5","DOI":"10.3390\/computation4010005","article-title":"Extracting conformational ensembles of small molecules from molecular dynamics simulations: Ampicillin as a test case","volume":"4","author":"Malloci","year":"2016","journal-title":"Computation"},{"issue":"8","key":"10.1016\/bs.mie.2025.10.001_bib153","doi-asserted-by":"crossref","first-page":"13997","DOI":"10.3390\/molecules200813997","article-title":"A database of force-field parameters, dynamics, and properties of antimicrobial compounds","volume":"20","author":"Malloci","year":"2015","journal-title":"Molecules (Basel, Switzerland)"},{"issue":"7","key":"10.1016\/bs.mie.2025.10.001_bib154","doi-asserted-by":"crossref","first-page":"1397","DOI":"10.1016\/j.bbamem.2019.05.004","article-title":"Molecular basis for the different interactions of congeneric substrates with the polyspecific transporter AcrB","volume":"1861","author":"Malvacio","year":"2019","journal-title":"Biochimica et Biophysica Acta (BBA)-Biomembranes"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib155","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1038\/s42004-024-01161-y","article-title":"Predicting permeation of compounds across the outer membrane of P. Aeruginosa using molecular descriptors","volume":"7","author":"Manrique","year":"2024","journal-title":"Communications Chemistry"},{"issue":"1-3","key":"10.1016\/bs.mie.2025.10.001_bib156","first-page":"168","article-title":"A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations","volume":"426","author":"Maragliano","year":"2006","journal-title":"EJCpl"},{"issue":"9","key":"10.1016\/bs.mie.2025.10.001_bib157","doi-asserted-by":"crossref","first-page":"6184","DOI":"10.1021\/acs.chemrev.8b00460","article-title":"Computational modeling of realistic cell membranes","volume":"119","author":"Marrink","year":"2019","journal-title":"Chemical Reviews"},{"key":"10.1016\/bs.mie.2025.10.001_bib158","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1146\/annurev.biophys.29.1.291","article-title":"Comparative protein structure modeling of genes and genomes","volume":"29","author":"Marti-Renom","year":"2000","journal-title":"Annual Review of Biophysics and Biomolecular Structure"},{"key":"10.1016\/bs.mie.2025.10.001_bib159","unstructured":"Marvin. (2012). Marvin 14.8.25.0. http:\/\/www.chemaxon.com."},{"issue":"36","key":"10.1016\/bs.mie.2025.10.001_bib160","doi-asserted-by":"crossref","first-page":"8133","DOI":"10.1021\/ja990935j","article-title":"Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies","volume":"121","author":"Massova","year":"1999","journal-title":"Journal of the American Chemical Society"},{"issue":"5","key":"10.1016\/bs.mie.2025.10.001_bib161","doi-asserted-by":"crossref","first-page":"1387","DOI":"10.1128\/AAC.44.5.1387-1390.2000","article-title":"Contributions of the AmpC beta-lactamase and the AcrAB multidrug efflux system in intrinsic resistance of escherichia coli K-12 to beta-lactams","volume":"44","author":"Mazzariol","year":"2000","journal-title":"Antimicrobial Agents and Chemotherapy"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib162","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/mBio.02785-20","article-title":"Predictive rules of efflux inhibition and avoidance in pseudomonas aeruginosa","volume":"12","author":"Mehla","year":"2021","journal-title":"MBio"},{"key":"10.1016\/bs.mie.2025.10.001_bib163","article-title":"Considerations in the use of ML interaction potentials for free energy calculations","author":"Mendible","year":"2024","journal-title":"Chemical Physics"},{"issue":"10","key":"10.1016\/bs.mie.2025.10.001_bib164","doi-asserted-by":"crossref","first-page":"2319","DOI":"10.1002\/jcc.21787","article-title":"MDAnalysis: A toolkit for the analysis of molecular dynamics simulations","volume":"32","author":"Michaud\u2010Agrawal","year":"2011","journal-title":"Journal of Computational Chemistry"},{"issue":"5","key":"10.1016\/bs.mie.2025.10.001_bib165","doi-asserted-by":"crossref","first-page":"1258","DOI":"10.1128\/JB.186.5.1258-1269.2004","article-title":"Differential impact of MexB mutations on substrate selectivity of the MexAB-OprM multidrug efflux pump of pseudomonas aeruginosa","volume":"186","author":"Middlemiss","year":"2004","journal-title":"Journal of Bacteriology"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib166","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1016\/j.str.2005.11.015","article-title":"Conformational flexibility in the multidrug efflux system protein AcrA","volume":"14","author":"Mikolosko","year":"2006","journal-title":"Structure (London, England: 1993)"},{"issue":"9","key":"10.1016\/bs.mie.2025.10.001_bib167","doi-asserted-by":"crossref","first-page":"3314","DOI":"10.1021\/ct300418h","article-title":"MMPBSA.py: An efficient program for End-State free energy calculations","volume":"8","author":"Miller","year":"2012","journal-title":"Journal of Chemical Theory and Computation"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib168","first-page":"85","article-title":"Calculation of protein-ligand binding free energy using smooth reaction path generation (SRPG) method: A comparison of the explicit water model, gb\/sa model and docking score function","volume":"23","author":"Mitomo","year":"2009","journal-title":"Genome Inform"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib169","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1021\/ct600085e","article-title":"Generalized born model with a simple, robust molecular volume correction","volume":"3","author":"Mongan","year":"2007","journal-title":"Journal of Chemical Theory and Computation"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib170","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.jsb.2011.01.014","article-title":"Designed ankyrin repeat protein binders for the crystallization of AcrB: Plasticity of the dominant interface","volume":"174","author":"Monroe","year":"2011","journal-title":"Journal of Structural Biology"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib171","first-page":"1932589","article-title":"Membrane models for molecular simulations of peripheral membrane proteins","volume":"6","author":"Moqadam","year":"2021","journal-title":"Advances in Physics: X"},{"key":"10.1016\/bs.mie.2025.10.001_bib172","doi-asserted-by":"crossref","first-page":"4644","DOI":"10.1039\/C8RA08441F","article-title":"Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: A review study","volume":"9","author":"Moradi","year":"2019","journal-title":"RSC Advances"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib173","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/mBio.03690-20","article-title":"Cryoelectron microscopy structures of AdeB illuminate mechanisms of simultaneous binding and exporting of substrates","volume":"12","author":"Morgan","year":"2021","journal-title":"MBio"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib174","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1002\/jcc.21973","article-title":"Analysis of lipid surface area in protein\u2013membrane systems combining voronoi tessellation and Monte Carlo integration methods","volume":"33","author":"Mori","year":"2013","journal-title":"Journal of Computational Chemistry"},{"issue":"16","key":"10.1016\/bs.mie.2025.10.001_bib175","doi-asserted-by":"crossref","first-page":"2785","DOI":"10.1002\/jcc.21256","article-title":"AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility","volume":"30","author":"Morris","year":"2009","journal-title":"Journal of Computational Chemistry"},{"issue":"6","key":"10.1016\/bs.mie.2025.10.001_bib176","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1016\/j.drudis.2015.01.003","article-title":"The impact of molecular dynamics on drug design: Applications for the characterization of ligand-macromolecule complexes","volume":"20","author":"Mortier","year":"2015","journal-title":"Drug Discovery Today"},{"issue":"9","key":"10.1016\/bs.mie.2025.10.001_bib177","doi-asserted-by":"crossref","first-page":"6086","DOI":"10.1021\/acs.chemrev.8b00608","article-title":"Characterization of lipid\u2013protein interactions and lipid-mediated modulation of membrane protein function through molecular simulation","volume":"119","author":"Muller","year":"2019","journal-title":"Chemical Reviews"},{"issue":"7108","key":"10.1016\/bs.mie.2025.10.001_bib178","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1038\/nature05076","article-title":"Crystal structures of a multidrug transporter reveal a functionally rotating mechanism","volume":"443","author":"Murakami","year":"2006","journal-title":"Nature"},{"issue":"6907","key":"10.1016\/bs.mie.2025.10.001_bib179","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nature01050","article-title":"Crystal structure of bacterial multidrug efflux transporter AcrB","volume":"419","author":"Murakami","year":"2002","journal-title":"Nature"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib180","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1529\/biophysj.104.048835","article-title":"Phosphatidylethanolamine-phosphatidylglycerol bilayer as a model of the inner bacterial membrane","volume":"88","author":"Murzyn","year":"2005","journal-title":"Biophysical Journal"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib181","doi-asserted-by":"crossref","first-page":"7284","DOI":"10.1038\/s41598-020-64129-7","article-title":"The effect of force-field parameters on cytochrome P450-membrane interactions: Structure and dynamics","volume":"10","author":"Mustafa","year":"2020","journal-title":"Scientific Reports"},{"issue":"7378","key":"10.1016\/bs.mie.2025.10.001_bib182","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1038\/nature10641","article-title":"Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket","volume":"480","author":"Nakashima","year":"2011","journal-title":"Nature"},{"issue":"20","key":"10.1016\/bs.mie.2025.10.001_bib183","doi-asserted-by":"crossref","first-page":"5853","DOI":"10.1128\/jb.178.20.5853-5859.1996","article-title":"Multidrug efflux pumps of gram-negative bacteria","volume":"178","author":"Nikaido","year":"1996","journal-title":"Journal of Bacteriology"},{"key":"10.1016\/bs.mie.2025.10.001_bib184","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1146\/annurev.biochem.78.082907.145923","article-title":"Multidrug resistance in bacteria","volume":"78","author":"Nikaido","year":"2009","journal-title":"Annual Review of Biochemistry"},{"issue":"7-8","key":"10.1016\/bs.mie.2025.10.001_bib185","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1016\/j.resmic.2018.03.001","article-title":"RND transporters in the living world","volume":"169","author":"Nikaido","year":"2018","journal-title":"Research in Microbiology"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib186","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1111\/j.1574-6976.2011.00290.x","article-title":"Broad-specificity efflux pumps and their role in multidrug resistance of Gram-negative bacteria","volume":"36","author":"Nikaido","year":"2012","journal-title":"FEMS Microbiology Reviews"},{"key":"10.1016\/bs.mie.2025.10.001_bib187","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1758-2946-3-33","article-title":"Open babel: An open chemical toolbox","volume":"3","author":"O'Boyle","year":"2011","journal-title":"Journal of Cheminformatics"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib188","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1002\/prot.20033","article-title":"Exploring protein native states and large-scale conformational changes with a modified generalized born model","volume":"55","author":"Onufriev","year":"2004","journal-title":"Proteins-Structure Function and Bioinformatics"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib189","doi-asserted-by":"crossref","first-page":"6919","DOI":"10.1038\/s41467-021-27146-2","article-title":"Structural and functional analysis of the promiscuous AcrB and AdeB efflux pumps suggests different drug binding mechanisms","volume":"12","author":"Ornik-Cha","year":"2021","journal-title":"Nature Communications"},{"key":"10.1016\/bs.mie.2025.10.001_bib190","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms13819","article-title":"Transport of lipophilic carboxylates is mediated by transmembrane helix 2 in multidrug transporter AcrB","volume":"7","author":"Oswald","year":"2016","journal-title":"Nature Communications"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib191","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1038\/s42256-022-00463-x","article-title":"The transformational role of GPU computing and deep learning in drug discovery","volume":"4","author":"Pandey","year":"2022","journal-title":"Nature Machine Intelligence"},{"key":"10.1016\/bs.mie.2025.10.001_bib192","article-title":"Boltz-2: Towards accurate and efficient binding affinity prediction","author":"Passaro","year":"2025","journal-title":"BioRxiv"},{"key":"10.1016\/bs.mie.2025.10.001_bib193","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1023\/B:JCAM.0000035186.90683.f2","article-title":"VEGA\u2013an open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming","volume":"18","author":"Pedretti","year":"2004","journal-title":"Journal of Computer-Aided Molecular Design"},{"issue":"5","key":"10.1016\/bs.mie.2025.10.001_bib194","doi-asserted-by":"crossref","first-page":"2112","DOI":"10.1073\/pnas.1012588108","article-title":"Structures of sequential open states in a symmetrical opening transition of the TolC exit duct","volume":"108","author":"Pei","year":"2011","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"13","key":"10.1016\/bs.mie.2025.10.001_bib195","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF chimera\u2014a visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"Journal of Computational Chemistry"},{"issue":"4","key":"10.1016\/bs.mie.2025.10.001_bib196","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1016\/j.str.2010.01.018","article-title":"Structural and dynamical insights into the opening mechanism of P. Aeruginosa OprM channel","volume":"18","author":"Phan","year":"2010","journal-title":"Structure (London, England: 1993)"},{"issue":"16","key":"10.1016\/bs.mie.2025.10.001_bib197","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1002\/jcc.20289","article-title":"Scalable molecular dynamics with NAMD","volume":"26","author":"Phillips","year":"2005","journal-title":"Journal of Computational Chemistry"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib198","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1128\/CMR.19.2.382-402.2006","article-title":"Clinically relevant chromosomally encoded multidrug resistance efflux pumps in bacteria","volume":"19","author":"Piddock","year":"2006","journal-title":"Clinical Microbiology Reviews"},{"issue":"18","key":"10.1016\/bs.mie.2025.10.001_bib199","doi-asserted-by":"crossref","first-page":"4331","DOI":"10.3390\/ijms20184331","article-title":"Molecular docking: Shifting paradigms in drug discovery","volume":"20","author":"Pinzi","year":"2019","journal-title":"International Journal of Molecular Sciences"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib200","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1038\/s41467-021-27726-2","article-title":"Pyridylpiperazine-based allosteric inhibitors of RND-type multidrug efflux pumps","volume":"13","author":"Pl\u00e9","year":"2022","journal-title":"Nature Communications"},{"issue":"7","key":"10.1016\/bs.mie.2025.10.001_bib201","doi-asserted-by":"crossref","first-page":"1556","DOI":"10.1016\/j.bbamem.2016.01.029","article-title":"Validating lipid force fields against experimental data: Progress, challenges and perspectives","volume":"1858","author":"Poger","year":"2016","journal-title":"Biochimica et Biophysica Acta (BBA)-Biomembranes"},{"key":"10.1016\/bs.mie.2025.10.001_bib202","article-title":"Recent advances in machine learning and Coarse-grained potentials for biomolecular simulations\u00a0and their applications","author":"Poma","year":"2025","journal-title":"ChemRxiv"},{"issue":"5","key":"10.1016\/bs.mie.2025.10.001_bib203","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1016\/S1369-5274(00)00242-3","article-title":"Multidrug resistance in Gram-negative bacteria","volume":"4","author":"Poole","year":"2001","journal-title":"Current Opinion in Microbiology"},{"issue":"22","key":"10.1016\/bs.mie.2025.10.001_bib204","doi-asserted-by":"crossref","first-page":"7363","DOI":"10.1128\/jb.175.22.7363-7372.1993","article-title":"Multiple antibiotic-resistance in Pseudomonas-Aeruginosa - evidence for involvement of an efflux operon","volume":"175","author":"Poole","year":"1993","journal-title":"Journal of Bacteriology"},{"issue":"13-14","key":"10.1016\/bs.mie.2025.10.001_bib205","doi-asserted-by":"crossref","first-page":"1894","DOI":"10.1002\/(SICI)1521-3773(19990712)38:13\/14<1894::AID-ANIE1894>3.0.CO;2-H","article-title":"Quantum chemical models (Nobel lecture)","volume":"38","author":"Pople","year":"1999","journal-title":"Angewandte Chemie International Edition"},{"issue":"17","key":"10.1016\/bs.mie.2025.10.001_bib206","doi-asserted-by":"crossref","first-page":"6893","DOI":"10.1073\/pnas.0902837106","article-title":"Trinity revealed: Stoichiometric complex assembly of a bacterial multidrug efflux pump","volume":"106","author":"Pos","year":"2009","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"10.1016\/bs.mie.2025.10.001_bib207","first-page":"1","article-title":"State-specific protein\u2013ligand complex structure prediction with a multiscale deep generative model","author":"Qiao","year":"2024","journal-title":"Quantitative Methods"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib208","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-017-08747-8","article-title":"Molecular rationale behind the differential substrate specificity of bacterial RND multi-drug transporters","volume":"7","author":"Ramaswamy","year":"2017","journal-title":"Scientific Reports"},{"key":"10.1016\/bs.mie.2025.10.001_bib209","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2018.01144","article-title":"Molecular determinants of the promiscuity of MexB and MexY multidrug transporters of pseudomonas aeruginosa","volume":"9","author":"Ramaswamy","year":"2018","journal-title":"Frontiers in Microbiology"},{"key":"10.1016\/bs.mie.2025.10.001_bib210","doi-asserted-by":"crossref","DOI":"10.3389\/fmolb.2021.760283","article-title":"Improving small-molecule force field parameters in ligand binding studies","volume":"8","author":"Raniolo","year":"2021","journal-title":"Frontiers in Molecular Biosciences"},{"issue":"26","key":"10.1016\/bs.mie.2025.10.001_bib211","doi-asserted-by":"crossref","first-page":"4674","DOI":"10.2174\/1381612811319260002","article-title":"Advances in binding free energies calculations: QM\/MM-based free energy perturbation method for drug design","volume":"19","author":"Rathore","year":"2013","journal-title":"Current Pharmaceutical Design"},{"key":"10.1016\/bs.mie.2025.10.001_bib212","doi-asserted-by":"crossref","first-page":"5565","DOI":"10.1038\/s41467-020-19397-2","article-title":"Perturbed structural dynamics underlie inhibition and altered efflux of the multidrug resistance pump AcrB","volume":"11","author":"Reading","year":"2020","journal-title":"Nature Communications"},{"issue":"12","key":"10.1016\/bs.mie.2025.10.001_bib213","doi-asserted-by":"crossref","first-page":"2562","DOI":"10.1021\/acs.jcim.5b00654","article-title":"Better informed distance geometry: Using what we know to improve conformation generation","volume":"55","author":"Riniker","year":"2015","journal-title":"Journal of Chemical Information and Modeling"},{"issue":"7","key":"10.1016\/bs.mie.2025.10.001_bib214","doi-asserted-by":"crossref","first-page":"3084","DOI":"10.1021\/ct400341p","article-title":"PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data","volume":"9","author":"Roe","year":"2013","journal-title":"Journal of Chemical Theory and Computation"},{"issue":"24","key":"10.1016\/bs.mie.2025.10.001_bib215","doi-asserted-by":"crossref","first-page":"3079","DOI":"10.2174\/15680266113136660220","article-title":"RND efflux pumps: Structural information translated into function and inhibition mechanisms","volume":"13","author":"Ruggerone","year":"2013","journal-title":"Current Topics in Medicinal Chemistry"},{"key":"10.1016\/bs.mie.2025.10.001_bib216","doi-asserted-by":"crossref","DOI":"10.5936\/csbj.201302008","article-title":"Molecular dynamics computer simulations of multidrug RND efflux pumps","volume":"5","author":"Ruggerone","year":"2013","journal-title":"Computational and Structural Biotechnology Journal"},{"issue":"7958","key":"10.1016\/bs.mie.2025.10.001_bib217","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1038\/s41586-023-05905-z","article-title":"Computational approaches streamlining drug discovery","volume":"616","author":"Sadybekov","year":"2023","journal-title":"Nature"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib218","doi-asserted-by":"crossref","first-page":"8000","DOI":"10.1038\/s41598-019-44318-9","article-title":"Role of lipid composition on the structural and mechanical features of axonal membranes: A molecular simulation study","volume":"9","author":"Saeedimasine","year":"2019","journal-title":"Scientific Reports"},{"key":"10.1016\/bs.mie.2025.10.001_bib219","series-title":"Alqumber MAA antimicrobial resistance: A growing serious threat for global public health","first-page":"1946","author":"Salam","year":"2023"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib220","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1006\/jmbi.1993.1626","article-title":"Comparative protein modelling by satisfaction of spatial restraints","volume":"234","author":"Sali","year":"1993","journal-title":"Journal of Molecular Biology"},{"issue":"9","key":"10.1016\/bs.mie.2025.10.001_bib221","doi-asserted-by":"crossref","first-page":"1582","DOI":"10.1002\/pro.5560030923","article-title":"Derivation of rules for comparative protein modeling from a database of protein structure alignments","volume":"3","author":"\u0160Ali","year":"1994","journal-title":"Protein Science"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib222","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1002\/prot.340230306","article-title":"Evaluation of comparative protein modeling by MODELLER","volume":"23","author":"\u0160ali","year":"1995","journal-title":"Proteins: Structure, Function, and Bioinformatics"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib223","doi-asserted-by":"crossref","first-page":"71","DOI":"10.3390\/pr9010071","article-title":"Molecular dynamics simulations in drug discovery and pharmaceutical development","volume":"9","author":"Salo-Ahen","year":"2020","journal-title":"Processes"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib224","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.1021\/acs.jctc.0c01006","article-title":"Accelerating AutoDock4 with GPUs and gradient-based local search","volume":"17","author":"Santos-Martins","year":"2021","journal-title":"Journal of Chemical Theory and Computation"},{"issue":"10","key":"10.1016\/bs.mie.2025.10.001_bib225","doi-asserted-by":"crossref","first-page":"2657","DOI":"10.1021\/ci3000453","article-title":"LAMBADA and InflateGRO2: Efficient membrane alignment and insertion of membrane proteins for molecular dynamics simulations","volume":"52","author":"Schmidt","year":"2012","journal-title":"Journal of Chemical Information and Modeling"},{"issue":"6","key":"10.1016\/bs.mie.2025.10.001_bib226","doi-asserted-by":"crossref","first-page":"2522","DOI":"10.1021\/acs.jcim.9b00269","article-title":"PACKMOL-Memgen: A simple-to-use, generalized workflow for membrane-protein\u2013lipid-bilayer system building","volume":"59","author":"Schott-Verdugo","year":"2019","journal-title":"Journal of Chemical Information and Modeling"},{"key":"10.1016\/bs.mie.2025.10.001_bib227","unstructured":"Schr\u00f6dinger, L., & DeLano, W. (2020). PyMOL."},{"issue":"6","key":"10.1016\/bs.mie.2025.10.001_bib228","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1000806","article-title":"Functional rotation of the transporter AcrB: Insights into drug extrusion from simulations","volume":"6","author":"Schulz","year":"2010","journal-title":"PLoS Computational Biology"},{"key":"10.1016\/bs.mie.2025.10.001_bib229","doi-asserted-by":"crossref","DOI":"10.1155\/2015\/487298","article-title":"Computational study of correlated domain motions in the AcrB efflux transporter","volume":"2015","author":"Schulz","year":"2015","journal-title":"Biomed Research International"},{"issue":"25","key":"10.1016\/bs.mie.2025.10.001_bib230","doi-asserted-by":"crossref","first-page":"8278","DOI":"10.1021\/jp200996x","article-title":"Role of water during the extrusion of substrates by the efflux transporter AcrB","volume":"115","author":"Schulz","year":"2011","journal-title":"The Journal of Physical Chemistry. B"},{"issue":"7","key":"10.1016\/bs.mie.2025.10.001_bib231","first-page":"4315","article-title":"Evidence of a substrate-discriminating entrance channel in the lower porter domain of the multidrug resistance efflux pump AcrB","volume":"60","author":"Schuster","year":"2016","journal-title":"WVJAA, Chemotherapy"},{"issue":"13","key":"10.1016\/bs.mie.2025.10.001_bib232","doi-asserted-by":"crossref","first-page":"3381","DOI":"10.1093\/nar\/gkg520","article-title":"Swiss-MODEL: An automated protein homology-modeling server","volume":"31","author":"Schwede","year":"2003","journal-title":"Nucleic Acids Research"},{"issue":"5791","key":"10.1016\/bs.mie.2025.10.001_bib233","doi-asserted-by":"crossref","first-page":"1295","DOI":"10.1126\/science.1131542","article-title":"Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism","volume":"313","author":"Seeger","year":"2006","journal-title":"Science (New York, N. Y.)"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib234","first-page":"106","article-title":"Drug export pathway of multidrug exporter AcrB revealed by DARPin inhibitors","volume":"5","author":"Sennhauser","year":"2007","journal-title":"PLoS Biology"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib235","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.jmb.2009.04.001","article-title":"Crystal structure of the multidrug exporter MexB from pseudomonas aeruginosa","volume":"389","author":"Sennhauser","year":"2009","journal-title":"Journal of Molecular Biology"},{"key":"10.1016\/bs.mie.2025.10.001_bib236","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1007\/s00894-019-3964-0","article-title":"Physical properties of model biological lipid bilayers: Insights from all-atom molecular dynamics simulations","volume":"25","author":"Shahane","year":"2019","journal-title":"Journal of Molecular Modeling"},{"key":"10.1016\/bs.mie.2025.10.001_bib237","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1007\/s10822-007-9133-z","article-title":"Epik: A software program for pk a prediction and protonation state generation for drug-like molecules","volume":"21","author":"Shelley","year":"2007","journal-title":"Journal of Computer-Aided Molecular Design"},{"issue":"11","key":"10.1016\/bs.mie.2025.10.001_bib238","doi-asserted-by":"crossref","first-page":"2507","DOI":"10.1110\/ps.062416606","article-title":"Statistical potential for assessment and prediction of protein structures","volume":"15","author":"Shen","year":"2006","journal-title":"Protein Science: A Publication of the Protein Society"},{"key":"10.1016\/bs.mie.2025.10.001_bib239","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1002\/jcc.540050204","article-title":"An approach to computing electrostatic charges for molecules","volume":"5","author":"Singh","year":"1984","journal-title":"Journal of Computational Chemistry"},{"issue":"13","key":"10.1016\/bs.mie.2025.10.001_bib240","doi-asserted-by":"crossref","first-page":"3509","DOI":"10.1073\/pnas.1602472113","article-title":"Molecular basis for inhibition of AcrB multidrug efflux pump by novel and powerful pyranopyridine derivatives","volume":"113","author":"Sjuts","year":"2016","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"36","key":"10.1016\/bs.mie.2025.10.001_bib241","doi-asserted-by":"crossref","first-page":"11124","DOI":"10.1021\/jp3059992","article-title":"LIPID11: A modular framework for lipid simulations using amber","volume":"116","author":"Skjevik","year":"2012","journal-title":"The Journal of Physical Chemistry. B"},{"issue":"18","key":"10.1016\/bs.mie.2025.10.001_bib242","doi-asserted-by":"crossref","first-page":"2296","DOI":"10.2174\/0929867311320180002","article-title":"Protein-ligand docking in the new millennium\u2013a retrospective of 10 years in the field","volume":"20","author":"Sousa","year":"2013","journal-title":"Current Medicinal Chemistry"},{"issue":"37","key":"10.1016\/bs.mie.2025.10.001_bib243","doi-asserted-by":"crossref","first-page":"9401","DOI":"10.1021\/ja981844+","article-title":"Continuum solvent studies of the stability of DNA, RNA, and Phosphoramidate-DNA helices","volume":"120","author":"Srinivasan","year":"1998","journal-title":"Journal of the American Chemical Society"},{"issue":"3","key":"10.1016\/bs.mie.2025.10.001_bib244","doi-asserted-by":"crossref","first-page":"232a","DOI":"10.1016\/j.bpj.2020.11.1540","article-title":"Estimating the accuracy of the MARTINI model towards the investigation of peripheral protein-membrane interactions","volume":"120","author":"Srinivasan","year":"2021","journal-title":"Biophysical Journal"},{"issue":"8","key":"10.1016\/bs.mie.2025.10.001_bib245","doi-asserted-by":"crossref","first-page":"767","DOI":"10.2174\/092986710790514453","article-title":"Towards accurate free energy calculations in ligand protein-binding studies","volume":"17","author":"Steinbrecher","year":"2010","journal-title":"Current Medicinal Chemistry"},{"issue":"6","key":"10.1016\/bs.mie.2025.10.001_bib246","doi-asserted-by":"crossref","first-page":"1583","DOI":"10.1021\/ct1007058","article-title":"Use of umbrella sampling to calculate the entrance\/exit pathway for Z-Pro-prolinal inhibitor in prolyl oligopeptidase","volume":"7","author":"St-Pierre","year":"2011","journal-title":"Journal of Chemical Theory and Computation"},{"issue":"20","key":"10.1016\/bs.mie.2025.10.001_bib247","doi-asserted-by":"crossref","first-page":"7290","DOI":"10.1128\/JB.00684-06","article-title":"Conformation of the AcrB multidrug efflux pump in mutants of the putative proton relay pathway","volume":"188","author":"Su","year":"2006","journal-title":"Journal of Bacteriology"},{"issue":"4","key":"10.1016\/bs.mie.2025.10.001_bib248","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/mBio.01295-19","article-title":"Cryo-electron microscopy structure of an acinetobacter baumannii multidrug efflux pump","volume":"10","author":"Su","year":"2019","journal-title":"MBio"},{"issue":"17","key":"10.1016\/bs.mie.2025.10.001_bib249","doi-asserted-by":"crossref","first-page":"7173","DOI":"10.1073\/pnas.0900693106","article-title":"The assembled structure of a complete tripartite bacterial multidrug efflux pump","volume":"106","author":"Symmons","year":"2009","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"15","key":"10.1016\/bs.mie.2025.10.001_bib250","doi-asserted-by":"crossref","first-page":"6559","DOI":"10.1073\/pnas.1001460107","article-title":"Mechanism of recognition of compounds of diverse structures by the multidrug efflux pump AcrB of escherichia coli","volume":"107","author":"Takatsuka","year":"2010","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"4","key":"10.1016\/bs.mie.2025.10.001_bib251","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1016\/j.jmb.2019.12.025","article-title":"Binding and transport of carboxylated drugs by the multidrug transporter AcrB","volume":"432","author":"Tam","year":"2020","journal-title":"Journal of Molecular Biology"},{"issue":"5","key":"10.1016\/bs.mie.2025.10.001_bib252","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1038\/s41579-019-0288-0","article-title":"The global preclinical antibacterial pipeline","volume":"18","author":"Theuretzbacher","year":"2020","journal-title":"Nature Reviews. Microbiology"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib253","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1021\/acs.jctc.9b00591","article-title":"ff19SB: Amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution","volume":"16","author":"Tian","year":"2019","journal-title":"Journal of Chemical Theory and Computation"},{"issue":"31","key":"10.1016\/bs.mie.2025.10.001_bib254","doi-asserted-by":"crossref","first-page":"32116","DOI":"10.1074\/jbc.M402230200","article-title":"AcrA, AcrB, and TolC of escherichia coli form a stable intermembrane multidrug efflux complex","volume":"279","author":"Tikhonova","year":"2004","journal-title":"Journal of Biological Chemistry"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib255","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1021\/ct700248k","article-title":"Performance of B3LYP density functional methods for a large set of organic molecules","volume":"4","author":"Tirado-Rives","year":"2008","journal-title":"Journal of Chemical Theory and Computation"},{"issue":"8","key":"10.1016\/bs.mie.2025.10.001_bib256","doi-asserted-by":"crossref","first-page":"2999","DOI":"10.1021\/cr9904009","article-title":"Quantum mechanical continuum solvation models","volume":"105","author":"Tomasi","year":"2005","journal-title":"Chemical Reviews"},{"issue":"10","key":"10.1016\/bs.mie.2025.10.001_bib257","doi-asserted-by":"crossref","first-page":"1953","DOI":"10.1016\/j.bbamem.2010.06.019","article-title":"Structure of reconstituted bacterial membrane efflux pump by cryo-electron tomography","volume":"1798","author":"Tr\u00e9pout","year":"2010","journal-title":"Biochimica et Biophysica Acta (BBA)\u00a0- Biomembranes"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib258","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","article-title":"Autodock vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading","volume":"31","author":"Trott","year":"2010","journal-title":"Journal of Computational Chemistry"},{"issue":"11","key":"10.1016\/bs.mie.2025.10.001_bib259","doi-asserted-by":"crossref","first-page":"2489","DOI":"10.1021\/ja9939385","article-title":"Molecular dynamics simulations of nucleic acids with a generalized born solvation model","volume":"122","author":"Tsui","year":"2000","journal-title":"Journal of the American Chemical Society"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib260","doi-asserted-by":"crossref","first-page":"1520","DOI":"10.1038\/s41467-019-09463-9","article-title":"Structures of the wild-type MexAB\u2013OprM tripartite pump reveal its complex formation and drug efflux mechanism","volume":"10","author":"Tsutsumi","year":"2019","journal-title":"Nature Communications"},{"issue":"16","key":"10.1016\/bs.mie.2025.10.001_bib261","doi-asserted-by":"crossref","first-page":"10142","DOI":"10.1021\/acs.chemrev.0c01111","article-title":"Machine learning force fields","volume":"121","author":"Unke","year":"2021","journal-title":"Chemical Reviews"},{"key":"10.1016\/bs.mie.2025.10.001_bib262","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.sbi.2020.08.006","article-title":"Systematic design of biomolecular force fields","volume":"67","author":"Van der Spoel","year":"2021","journal-title":"Current Opinion in Structural Biology"},{"issue":"28","key":"10.1016\/bs.mie.2025.10.001_bib263","doi-asserted-by":"crossref","first-page":"10704","DOI":"10.1021\/ja202666x","article-title":"Effect of the F610A mutation on substrate extrusion in the AcrB transporter: Explanation and rationale by molecular dynamics simulations","volume":"133","author":"Vargiu","year":"2011","journal-title":"Journal of the American Chemical Society"},{"issue":"9","key":"10.1016\/bs.mie.2025.10.001_bib264","doi-asserted-by":"crossref","first-page":"1966","DOI":"10.1002\/cmdc.201402203","article-title":"Atomistic-level portrayal of Drug-DNA interplay: A history of courtships and meetings revealed by molecular simulations","volume":"9","author":"Vargiu","year":"2014","journal-title":"ChemMedChem"},{"issue":"50","key":"10.1016\/bs.mie.2025.10.001_bib265","doi-asserted-by":"crossref","first-page":"20637","DOI":"10.1073\/pnas.1218348109","article-title":"Multidrug binding properties of the AcrB efflux pump characterized by molecular dynamics simulations","volume":"109","author":"Vargiu","year":"2012","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"10.1016\/bs.mie.2025.10.001_bib266","article-title":"The structural and functional study of efflux pumps belonging to the RND transporters family from Gram-negative bacteria","volume":"11","author":"Vargiu","year":"2022","journal-title":"MDPI"},{"issue":"7-8","key":"10.1016\/bs.mie.2025.10.001_bib267","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1016\/j.resmic.2017.12.001","article-title":"Computer simulations of the activity of RND efflux pumps","volume":"169","author":"Vargiu","year":"2018","journal-title":"Research in Microbiology"},{"issue":"10","key":"10.1016\/bs.mie.2025.10.001_bib268","doi-asserted-by":"crossref","first-page":"6224","DOI":"10.1128\/AAC.03283-14","article-title":"Molecular mechanism of MBX2319 inhibition of escherichia coli AcrB multidrug efflux pump and comparison with other inhibitors","volume":"58","author":"Vargiu","year":"2014","journal-title":"Antimicrobial Agents and Chemotherapy"},{"issue":"10","key":"10.1016\/bs.mie.2025.10.001_bib269","first-page":"880","article-title":"There is a baby in the bath water: AcrB contamination is a major problem in membrane-protein crystallization","volume":"64","author":"Veesler","year":"2008","journal-title":"Acta Crystallographica Section F: Structural Biology and Crystallization Communications"},{"issue":"1","key":"10.1016\/bs.mie.2025.10.001_bib270","doi-asserted-by":"crossref","first-page":"1062","DOI":"10.1038\/s42003-022-04024-1","article-title":"A framework for dissecting affinities of multidrug efflux transporter AcrB to fluoroquinolones","volume":"5","author":"Vergalli","year":"2022","journal-title":"Communications Biology"},{"issue":"5","key":"10.1016\/bs.mie.2025.10.001_bib271","first-page":"1182","article-title":"In silico high-throughput virtual screening and molecular dynamics simulation study to identify inhibitor for AdeABC efflux pump of acinetobacter baumannii","volume":"36","author":"Verma","year":"2018","journal-title":"VJJoBS, Dynamics"},{"key":"10.1016\/bs.mie.2025.10.001_bib272","first-page":"302","article-title":"Substrate binding accelerates the conformational transitions and substrate dissociation in multidrug efflux transporter AcrB","volume":"6","author":"Wang","year":"2015","journal-title":"Frontiers in Microbiology"},{"key":"10.1016\/bs.mie.2025.10.001_bib273","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1016\/j.csbj.2022.02.004","article-title":"Protein-ligand binding affinity prediction based on profiles of intermolecular contacts","volume":"20","author":"Wang","year":"2022","journal-title":"Computational and Structural Biotechnology Journal"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib274","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/j.jmgm.2005.12.005","article-title":"Automatic atom type and bond type perception in molecular mechanical calculations","volume":"25","author":"Wang","year":"2006","journal-title":"Journal of Molecular Graphics & Modelling"},{"issue":"9","key":"10.1016\/bs.mie.2025.10.001_bib275","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1002\/jcc.20035","article-title":"Development and testing of a general amber force field","volume":"25","author":"Wang","year":"2004","journal-title":"Journal of Computational Chemistry"},{"issue":"4","key":"10.1016\/bs.mie.2025.10.001_bib276","doi-asserted-by":"crossref","first-page":"2044","DOI":"10.1021\/acs.jcim.0c00025","article-title":"Improving conformer generation for small rings and macrocycles based on distance geometry and experimental torsional-angle preferences","volume":"60","author":"Wang","year":"2020","journal-title":"Journal of Chemical Information and Modeling"},{"key":"10.1016\/bs.mie.2025.10.001_bib277","article-title":"An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump","volume":"6","author":"Wang","year":"2017","journal-title":"Elife"},{"issue":"6","key":"10.1016\/bs.mie.2025.10.001_bib278","doi-asserted-by":"crossref","first-page":"3149","DOI":"10.1039\/C9CP06303J","article-title":"Combined strategies in structure-based virtual screening","volume":"22","author":"Wang","year":"2020","journal-title":"Physical Chemistry Chemical Physics"},{"key":"10.1016\/bs.mie.2025.10.001_bib279","article-title":"Boltz-1 democratizing biomolecular interaction modeling","author":"Wohlwend","year":"2024","journal-title":"BioRxiv"},{"issue":"19","key":"10.1016\/bs.mie.2025.10.001_bib280","doi-asserted-by":"crossref","first-page":"6825","DOI":"10.1073\/pnas.0409005102","article-title":"Calculation of absolute protein-ligand binding free energy from computer simulations","volume":"102","author":"Woo","year":"2005","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"27","key":"10.1016\/bs.mie.2025.10.001_bib281","doi-asserted-by":"crossref","first-page":"1997","DOI":"10.1002\/jcc.23702","article-title":"CHARMM-GUI membrane builder toward realistic biological membrane simulations","volume":"35","author":"Wu","year":"2014","journal-title":"Journal of Computational Chemistry"},{"issue":"20","key":"10.1016\/bs.mie.2025.10.001_bib282","doi-asserted-by":"crossref","first-page":"17910","DOI":"10.1074\/jbc.M111.238535","article-title":"Funnel-like hexameric assembly of the periplasmic adapter protein in the tripartite multidrug efflux pump in Gram-negative bacteria","volume":"286","author":"Xu","year":"2011","journal-title":"Journal of Biological Chemistry"},{"issue":"15","key":"10.1016\/bs.mie.2025.10.001_bib283","doi-asserted-by":"crossref","first-page":"11740","DOI":"10.1074\/jbc.M111.329375","article-title":"Assembly and channel opening of outer membrane protein in tripartite drug efflux pumps of Gram-negative bacteria","volume":"287","author":"Xu","year":"2012","journal-title":"The Journal of Biological Chemistry"},{"issue":"2","key":"10.1016\/bs.mie.2025.10.001_bib284","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1021\/acs.jctc.3c00920","article-title":"Development and comprehensive benchmark of a High-Quality AMBER-Consistent small molecule force field with broad chemical space coverage for molecular modeling and free energy calculation","volume":"20","author":"Xue","year":"2023","journal-title":"Journal of Chemical Theory and Computation"},{"key":"10.1016\/bs.mie.2025.10.001_bib285","doi-asserted-by":"crossref","first-page":"327","DOI":"10.3389\/fmicb.2015.00327","article-title":"Structural basis of RND-type multidrug exporters","volume":"6","author":"Yamaguchi","year":"2015","journal-title":"Frontiers in Microbiology"},{"key":"10.1016\/bs.mie.2025.10.001_bib286","doi-asserted-by":"crossref","DOI":"10.1016\/j.mib.2022.102179","article-title":"Making sense of drug-efflux transporters in the physiological environment","volume":"69","author":"Zgurskaya","year":"2022","journal-title":"Current Opinion in Microbiology"},{"key":"10.1016\/bs.mie.2025.10.001_bib287","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.mib.2021.03.009","article-title":"Bacterial efflux transporters\u2019 polyspecificity\u2013a gift and a curse?","volume":"61","author":"Zgurskaya","year":"2021","journal-title":"Current Opinion in Microbiology"},{"issue":"13","key":"10.1016\/bs.mie.2025.10.001_bib288","doi-asserted-by":"crossref","first-page":"7190","DOI":"10.1073\/pnas.96.13.7190","article-title":"Bypassing the periplasm: Reconstitution of the AcrAB multidrug efflux pump of escherichia coli","volume":"96","author":"Zgurskaya","year":"1999","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"10.1016\/bs.mie.2025.10.001_bib289","doi-asserted-by":"crossref","first-page":"100","DOI":"10.3389\/fmicb.2015.00100","article-title":"Mechanism of coupling drug transport reactions located in two different membranes","volume":"6","author":"Zgurskaya","year":"2015","journal-title":"Frontiers in Microbiology"},{"issue":"5","key":"10.1016\/bs.mie.2025.10.001_bib290","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1016\/j.bbapap.2008.10.010","article-title":"Structural and functional diversity of bacterial membrane fusion proteins","volume":"1794","author":"Zgurskaya","year":"2009","journal-title":"Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics"},{"issue":"14","key":"10.1016\/bs.mie.2025.10.001_bib291","doi-asserted-by":"crossref","first-page":"4338","DOI":"10.1021\/acs.jctc.3c00214","article-title":"Artificial intelligence enhanced molecular simulations","volume":"19","author":"Zhang","year":"2023","journal-title":"Journal of Chemical Theory and Computation"},{"key":"10.1016\/bs.mie.2025.10.001_bib292","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2017.02095","article-title":"Hoisting-loop in bacterial multidrug exporter AcrB is a highly flexible hinge that enables the large motion of the subdomains","volume":"8","author":"Zwama","year":"2017","journal-title":"Frontiers in Microbiology"},{"issue":"8","key":"10.1016\/bs.mie.2025.10.001_bib293","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1063\/1.1740409","article-title":"High\u2010temperature equation of state by a perturbation method. I. nonpolar gases","volume":"22","author":"Zwanzig","year":"1954","journal-title":"The Journal of Chemical Physics"}],"container-title":["Methods in Enzymology","Bacterial Efflux Systems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0076687925003933?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0076687925003933?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T18:44:23Z","timestamp":1766083463000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0076687925003933"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"ISBN":["9780443429590"],"references-count":293,"URL":"https:\/\/doi.org\/10.1016\/bs.mie.2025.10.001","relation":{},"ISSN":["0076-6879"],"issn-type":[{"type":"print","value":"0076-6879"}],"subject":[],"published":{"date-parts":[[2025]]}}}