{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,19]],"date-time":"2026-09-19T12:15:01Z","timestamp":1789820101731,"version":"4.0.1"},"reference-count":99,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Computers in Biology and Medicine"],"published-print":{"date-parts":[[2025,3]]},"DOI":"10.1016\/j.compbiomed.2025.109727","type":"journal-article","created":{"date-parts":[[2025,1,25]],"date-time":"2025-01-25T03:10:35Z","timestamp":1737774635000},"page":"109727","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":5,"special_numbering":"C","title":["Pharmacophore-guided computational modeling of quinolone-ATPase conjugate inhibitors targeting DNA GyrB subunit of Staphylococcus aureus"],"prefix":"10.1016","volume":"186","author":[{"given":"Md.","family":"Al Amin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-1465-6138","authenticated-orcid":false,"given":"Md. Sakhawat","family":"Hossain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Md. Kawsar","family":"Habib","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Faria Farzana","family":"Perveen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sahinur Islam","family":"Sabuj","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hasan","family":"Imam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sirajul","family":"Islam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5113-2527","authenticated-orcid":false,"given":"Shahin","family":"Mahmud","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"13","key":"10.1016\/j.compbiomed.2025.109727_bib1","doi-asserted-by":"crossref","DOI":"10.3390\/healthcare11131946","article-title":"Antimicrobial resistance: a growing serious threat for global public health","volume":"11","author":"Salam","year":"2023","journal-title":"Healthcare"},{"issue":"12","key":"10.1016\/j.compbiomed.2025.109727_bib2","doi-asserted-by":"crossref","DOI":"10.1016\/j.jiph.2021.10.020","article-title":"Antibiotic resistance in microbes: history, mechanisms, therapeutic strategies and future prospects","volume":"14","author":"Uddin","year":"2021","journal-title":"J. Infec. Publ. Health"},{"issue":"10","key":"10.1016\/j.compbiomed.2025.109727_bib3","doi-asserted-by":"crossref","DOI":"10.3390\/pathogens10101310","article-title":"Bacterial antibiotic resistance: the most critical pathogens","volume":"10","author":"Mancuso","year":"2021","journal-title":"Pathogens"},{"key":"10.1016\/j.compbiomed.2025.109727_bib4","doi-asserted-by":"crossref","DOI":"10.2147\/IDR.S428103","article-title":"Methicillin resistant Staphylococcus aureus: molecular mechanisms underlying drug resistance development and novel strategies to combat","volume":"16","author":"Abebe","year":"2023","journal-title":"Infect. Drug Resist."},{"issue":"4","key":"10.1016\/j.compbiomed.2025.109727_bib5","doi-asserted-by":"crossref","DOI":"10.2144\/fsoa-2019-0122","article-title":"Antibiotic resistance pattern of Staphylococcus aureus with reference to MRSA isolates from pediatric patients","volume":"6","author":"Gurung","year":"2020","journal-title":"Futur. Sci. OA"},{"key":"10.1016\/j.compbiomed.2025.109727_bib6","unstructured":"\u201cMethicillin Resistant Staphylococcus Aureus Infection - an overview | ScienceDirect Topics.\u201d https:\/\/www.sciencedirect.com\/topics\/medicine-and-dentistry\/methicillin-resistant-staphylococcus-aureus-infection (accessed Dec. 01, 2024).."},{"key":"10.1016\/j.compbiomed.2025.109727_bib7","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2021.684515","article-title":"Brief overview of approaches and challenges in new antibiotic development: a focus on drug repurposing","volume":"11","author":"Boyd","year":"2021","journal-title":"Front. Cell. Infect. Microbiol."},{"issue":"9","key":"10.1016\/j.compbiomed.2025.109727_bib8","doi-asserted-by":"crossref","DOI":"10.1016\/j.drudis.2021.02.014","article-title":"Challenges and opportunities in the discovery, development, and commercialization of pathogen-targeted antibiotics","volume":"26","author":"Altarac","year":"2021","journal-title":"Drug Discov. Today"},{"issue":"10","key":"10.1016\/j.compbiomed.2025.109727_bib9","doi-asserted-by":"crossref","DOI":"10.1038\/s41570-021-00313-1","article-title":"Towards the sustainable discovery and development of new antibiotics","volume":"5","author":"Miethke","year":"2021","journal-title":"Nat. Rev. Chem"},{"issue":"7958","key":"10.1016\/j.compbiomed.2025.109727_bib10","doi-asserted-by":"crossref","DOI":"10.1038\/s41586-023-05905-z","article-title":"Computational approaches streamlining drug discovery","volume":"616","author":"Sadybekov","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.compbiomed.2025.109727_bib11","article-title":"Molecular modeling in drug discovery","volume":"29","author":"Adelusi","year":"2022","journal-title":"Inform. Med. Unlocked"},{"issue":"21","key":"10.1016\/j.compbiomed.2025.109727_bib12","doi-asserted-by":"crossref","DOI":"10.1021\/acs.jctc.3c00814","article-title":"Integrated molecular modeling and machine learning for drug design","volume":"19","author":"Xia","year":"2023","journal-title":"J. Chem. Theor. Comput."},{"issue":"7","key":"10.1016\/j.compbiomed.2025.109727_bib13","doi-asserted-by":"crossref","first-page":"13384","DOI":"10.3390\/molecules200713384","article-title":"Molecular docking and structure-based drug design strategies","volume":"20","author":"Ferreira","year":"2015","journal-title":"Molecules"},{"issue":"1","key":"10.1016\/j.compbiomed.2025.109727_bib14","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/s40360-024-00804-z","article-title":"In silico molecular targets, docking, dynamics simulation and physiologically based pharmacokinetics modeling of oritavancin","volume":"25","author":"Fatoki","year":"2024","journal-title":"BMC Pharmacol. Toxicol."},{"key":"10.1016\/j.compbiomed.2025.109727_bib15","doi-asserted-by":"crossref","DOI":"10.3389\/fchem.2020.00093","article-title":"In silico strategies to support fragment-to-lead optimization in drug discovery","volume":"8","author":"de Souza Neto","year":"2020","journal-title":"Front. Chem."},{"issue":"5","key":"10.1016\/j.compbiomed.2025.109727_bib16","doi-asserted-by":"crossref","DOI":"10.2144\/fsoa-2022-0085","article-title":"Updates on drug designing approach through computational strategies: a review","volume":"9","author":"Azad","year":"2023","journal-title":"Future Science OA"},{"issue":"8","key":"10.1016\/j.compbiomed.2025.109727_bib17","doi-asserted-by":"crossref","DOI":"10.3390\/pharmaceutics14081749","article-title":"Fluoroquinolones hybrid molecules as promising antibacterial agents in the fight against antibacterial resistance","volume":"14","author":"Lungu","year":"2022","journal-title":"Pharmaceutics"},{"key":"10.1016\/j.compbiomed.2025.109727_bib18","doi-asserted-by":"crossref","DOI":"10.1016\/j.ejmech.2022.115026","article-title":"Current scenario of quinolone hybrids with potential antibacterial activity against ESKAPE pathogens","volume":"247","author":"Gao","year":"2023","journal-title":"Eur. J. Med. Chem."},{"issue":"1","key":"10.1016\/j.compbiomed.2025.109727_bib19","doi-asserted-by":"crossref","DOI":"10.1128\/CMR.00115-20","article-title":"New \u03b2-lactam\u2013\u03b2-lactamase inhibitor combinations","volume":"34","author":"Yahav","year":"2021","journal-title":"Clin. Microbiol. Rev."},{"issue":"5","key":"10.1016\/j.compbiomed.2025.109727_bib20","doi-asserted-by":"crossref","DOI":"10.1021\/acs.jmedchem.9b01279","article-title":"\u03b2-Lactamase inhibitors to restore the efficacy of antibiotics against superbugs","volume":"63","author":"Gonz\u00e1lez-Bello","year":"2020","journal-title":"J. Med. Chem."},{"key":"10.1016\/j.compbiomed.2025.109727_bib21","doi-asserted-by":"crossref","DOI":"10.1016\/j.coche.2021.100721","article-title":"Computer-aided retrosynthetic design: fundamentals, tools, and outlook","volume":"35","author":"Sun","year":"2022","journal-title":"Curr. Opin. Chem. Eng."},{"key":"10.1016\/j.compbiomed.2025.109727_bib22","unstructured":"IBM RXN for Chemistry.\u201d https:\/\/rxn.res.ibm.com\/rxn\/robo-rxn\/welcome (accessed Jun. 27, 2024).."},{"key":"10.1016\/j.compbiomed.2025.109727_bib23","doi-asserted-by":"crossref","DOI":"10.1016\/j.jmgm.2023.108429","article-title":"Structure-based pharmacophore modeling 1. Automated random pharmacophore model generation","volume":"121","author":"Szwabowski","year":"2023","journal-title":"J. Mol. Graph. Model."},{"issue":"2","key":"10.1016\/j.compbiomed.2025.109727_bib24","doi-asserted-by":"crossref","DOI":"10.3390\/biomedicines11020371","article-title":"DNA gyrase as a target for quinolones","volume":"11","author":"Spencer","year":"2023","journal-title":"Biomedicines"},{"key":"10.1016\/j.compbiomed.2025.109727_bib25","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkaa1038","article-title":"RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences","author":"Burley","year":"2021","journal-title":"Nucleic Acids Res."},{"issue":"5","key":"10.1016\/j.compbiomed.2025.109727_bib26","doi-asserted-by":"crossref","DOI":"10.3390\/ph15050646","article-title":"Drug design by pharmacophore and virtual screening approach","volume":"15","author":"Giordano","year":"2022","journal-title":"Pharmaceuticals"},{"issue":"24","key":"10.1016\/j.compbiomed.2025.109727_bib27","doi-asserted-by":"crossref","DOI":"10.1016\/j.bmcl.2011.10.010","article-title":"Pyrrolamide DNA gyrase inhibitors: optimization of antibacterial activity and efficacy","volume":"21","author":"Sherer","year":"2011","journal-title":"Bioorg. Med. Chem. Lett"},{"issue":"3","key":"10.1016\/j.compbiomed.2025.109727_bib28","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.05485-11","article-title":"Pyrrolamide DNA gyrase inhibitors: fragment-based nuclear magnetic resonance screening to identify antibacterial agents","volume":"56","author":"Eakin","year":"2012","journal-title":"Antimicrob. Agents Chemother."},{"issue":"1","key":"10.1016\/j.compbiomed.2025.109727_bib29","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1021\/ci049885e","article-title":"LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters","volume":"45","author":"Wolber","year":"2005","journal-title":"J. Chem. Inf. Model."},{"issue":"4","key":"10.1016\/j.compbiomed.2025.109727_bib30","doi-asserted-by":"crossref","first-page":"e1468","DOI":"10.1002\/wcms.1468","article-title":"Next generation 3D pharmacophore modeling","volume":"10","author":"Schaller","year":"2020","journal-title":"Wiley Interdiscip. Rev. Comput. Mol. Sci."},{"issue":"1","key":"10.1016\/j.compbiomed.2025.109727_bib31","doi-asserted-by":"crossref","DOI":"10.3390\/molecules25010107","article-title":"Structure-based virtual screening and biological evaluation of peptide inhibitors for polo-box domain","volume":"25","author":"Yan","year":"2020","journal-title":"Molecules"},{"key":"10.1016\/j.compbiomed.2025.109727_bib32","unstructured":"Goodness-of-Fit.\u201d https:\/\/www.investopedia.com\/terms\/g\/goodness-of-fit.asp (accessed Jun. 27, 2024).."},{"key":"10.1016\/j.compbiomed.2025.109727_bib33","series-title":"Mean Average Precision (mAP) Explained: Everything You Need to Know","author":"Shah","year":"2022"},{"issue":"4","key":"10.1016\/j.compbiomed.2025.109727_bib34","doi-asserted-by":"crossref","DOI":"10.1016\/j.heliyon.2021.e06605","article-title":"Pharmacophore model, docking, QSAR, and molecular dynamics simulation studies of substituted cyclic imides and herbal medicines as COX-2 inhibitors","volume":"7","author":"Moussa","year":"2021","journal-title":"Heliyon"},{"issue":"24","key":"10.1016\/j.compbiomed.2025.109727_bib35","doi-asserted-by":"crossref","DOI":"10.3390\/ijms232416122","article-title":"Pharmacophore-oriented identification of potential leads as CCR5 inhibitors to block HIV cellular entry","volume":"23","author":"Singh","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.compbiomed.2025.109727_bib36","series-title":"A Guide to Applied Machine Learning for Biologists","article-title":"The Python programming language","author":"Bin Mehare","year":"2023"},{"issue":"W1","key":"10.1016\/j.compbiomed.2025.109727_bib37","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1093\/nar\/gks378","article-title":"ZINCPharmer: pharmacophore search of the ZINC database","volume":"40","author":"Koes","year":"2012","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"10.1016\/j.compbiomed.2025.109727_bib38","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1021\/ci049714+","article-title":"Zinc - a free database of commercially available compounds for virtual screening","volume":"45","author":"Irwin","year":"2005","journal-title":"J. Chem. Inf. Model."},{"issue":"D1","key":"10.1016\/j.compbiomed.2025.109727_bib39","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkr777","article-title":"ChEMBL: a large-scale bioactivity database for drug discovery","volume":"40","author":"Gaulton","year":"2012","journal-title":"Nucleic Acids Res."},{"issue":"3","key":"10.1016\/j.compbiomed.2025.109727_bib40","doi-asserted-by":"crossref","DOI":"10.2174\/1573409916666200620194143","article-title":"Multi-objective genetic algorithm for de novo drug design (MoGADdrug)","volume":"17","author":"Devi","year":"2020","journal-title":"Curr. Comput. Aided Drug Des."},{"issue":"7","key":"10.1016\/j.compbiomed.2025.109727_bib41","doi-asserted-by":"crossref","DOI":"10.1021\/acs.jcim.3c00610","article-title":"AlvaBuilder: a software for de novo molecular design","volume":"64","author":"Mauri","year":"2024","journal-title":"J. Chem. Inf. Model."},{"issue":"21","key":"10.1016\/j.compbiomed.2025.109727_bib42","doi-asserted-by":"crossref","DOI":"10.3390\/ijms232112882","article-title":"Alvascience: a new software suite for the QSAR workflow applied to the blood\u2013brain barrier permeability","volume":"23","author":"Mauri","year":"2022","journal-title":"Int. J. Mol. Sci."},{"issue":"10","key":"10.1016\/j.compbiomed.2025.109727_bib43","doi-asserted-by":"crossref","first-page":"1719","DOI":"10.1039\/C9MD00120D","article-title":"Quinolone antibiotics","volume":"10","author":"Pham","year":"2019","journal-title":"Medchemcomm"},{"key":"10.1016\/j.compbiomed.2025.109727_bib44","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1016\/j.ejmech.2013.01.057","article-title":"Antibacterial action of quinolones: from target to network","volume":"66","author":"Cheng","year":"2013","journal-title":"Eur. J. Med. Chem."},{"key":"10.1016\/j.compbiomed.2025.109727_bib45","unstructured":"Quinolone Derivative - an overview | ScienceDirect Topics.\u201d https:\/\/www.sciencedirect.com\/topics\/pharmacology-toxicology-and-pharmaceutical-science\/quinolone-derivative (accessed Jun. 27, 2024).."},{"issue":"1","key":"10.1016\/j.compbiomed.2025.109727_bib46","doi-asserted-by":"crossref","DOI":"10.1186\/s13321-023-00678-z","article-title":"Critical assessment of synthetic accessibility scores in computer-assisted synthesis planning","volume":"15","author":"Skoraczy\u0144ski","year":"2023","journal-title":"J. Cheminf."},{"key":"10.1016\/j.compbiomed.2025.109727_bib47","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1758-2946-1-8","article-title":"Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions","volume":"1","author":"Ertl","year":"2009","journal-title":"J. Cheminf."},{"key":"10.1016\/j.compbiomed.2025.109727_bib48","doi-asserted-by":"crossref","DOI":"10.1016\/j.ejmech.2012.06.024","article-title":"Is chemical synthetic accessibility computationally predictable for drug and lead-like molecules? A comparative assessment between medicinal and computational chemists","volume":"54","author":"Bonnet","year":"2012","journal-title":"Eur. J. Med. Chem."},{"issue":"1","key":"10.1016\/j.compbiomed.2025.109727_bib49","doi-asserted-by":"crossref","DOI":"10.1186\/s13321-023-00742-8","article-title":"Integrating synthetic accessibility with AI-based generative drug design","volume":"15","author":"Parrot","year":"2023","journal-title":"J. Cheminf."},{"issue":"5","key":"10.1016\/j.compbiomed.2025.109727_bib50","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1021\/ml500069w","article-title":"Oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad spectrum antibacterial agents","volume":"5","author":"Singh","year":"2014","journal-title":"ACS Med. Chem. Lett."},{"issue":"W1","key":"10.1016\/j.compbiomed.2025.109727_bib51","doi-asserted-by":"crossref","first-page":"W363","DOI":"10.1093\/nar\/gky473","article-title":"CASTp 3.0: computed atlas of surface topography of proteins","volume":"46","author":"Tian","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiomed.2025.109727_bib52","series-title":"Dassault Systemes BIOVIA, Discovery Studio Modelling Environment, Release 4.5","author":"Studio","year":"2015"},{"issue":"2","key":"10.1016\/j.compbiomed.2025.109727_bib53","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":"J. Comput. Chem."},{"key":"10.1016\/j.compbiomed.2025.109727_bib54","doi-asserted-by":"crossref","DOI":"10.1038\/srep42717","article-title":"SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules","author":"Daina","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.compbiomed.2025.109727_bib55","doi-asserted-by":"crossref","DOI":"10.1186\/1741-7007-9-71","article-title":"Molecular dynamics simulations and drug discovery","volume":"9","author":"Durrant","year":"2011","journal-title":"BMC Biol."},{"issue":"1","key":"10.1016\/j.compbiomed.2025.109727_bib56","doi-asserted-by":"crossref","DOI":"10.1007\/s10822-011-9517-y","article-title":"The future of molecular dynamics simulations in drug discovery","volume":"26","author":"Borhani","year":"2012","journal-title":"J. Comput. Aided Mol. Des."},{"issue":"2\u20133","key":"10.1016\/j.compbiomed.2025.109727_bib57","article-title":"Molecular simulation of hydrogen storage and transport in cellulose","volume":"47","author":"Stalker","year":"2021","journal-title":"Mol. Simulat."},{"issue":"5","key":"10.1016\/j.compbiomed.2025.109727_bib58","doi-asserted-by":"crossref","DOI":"10.1063\/1.3548869","article-title":"Sources of the deficiencies in the popular SPCE and TIP3P models of water","volume":"134","author":"Kiss","year":"2011","journal-title":"J. Chem. Phys."},{"issue":"4","key":"10.1016\/j.compbiomed.2025.109727_bib59","doi-asserted-by":"crossref","DOI":"10.1021\/acs.jctc.7b00028","article-title":"How molecular size impacts RMSD applications in molecular dynamics simulations","volume":"13","author":"Sargsyan","year":"2017","journal-title":"J. Chem. Theor. Comput."},{"issue":"3","key":"10.1016\/j.compbiomed.2025.109727_bib60","doi-asserted-by":"crossref","DOI":"10.1111\/j.1432-1033.1987.tb11173.x","article-title":"Stereospecific assignments of side\u2010chain protons and characterization of torsion angles in Eglin c","volume":"164","author":"Hyberts","year":"1987","journal-title":"Eur. J. Biochem."},{"key":"10.1016\/j.compbiomed.2025.109727_bib61","doi-asserted-by":"crossref","DOI":"10.1155\/2012\/173521","article-title":"Relaxation estimation of RMSD in molecular dynamics immunosimulations","volume":"2012","author":"Schreiner","year":"2012","journal-title":"Comput. Math. Methods Med."},{"issue":"29","key":"10.1016\/j.compbiomed.2025.109727_bib62","doi-asserted-by":"crossref","DOI":"10.1021\/jp302103t","article-title":"A comparison of multiscale methods for the analysis of molecular dynamics simulations","volume":"116","author":"Benson","year":"2012","journal-title":"J. Phys. Chem. B"},{"issue":"1","key":"10.1016\/j.compbiomed.2025.109727_bib63","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-017-15930-4","article-title":"Characterizing the conformational landscape of MDM2-binding p53 peptides using Molecular Dynamics simulations","volume":"7","author":"Yadahalli","year":"2017","journal-title":"Sci. Rep."},{"issue":"12","key":"10.1016\/j.compbiomed.2025.109727_bib64","doi-asserted-by":"crossref","DOI":"10.1002\/minf.202000216","article-title":"SMARTS.plus \u2013 a toolbox for chemical pattern design","volume":"39","author":"Ehrt","year":"2020","journal-title":"Molecular Informatics"},{"key":"10.1016\/j.compbiomed.2025.109727_bib65","unstructured":"Thieme trains IBM RXN for Chemistry with high-quality data - IBM Research.\u201d https:\/\/research.ibm.com\/blog\/thieme-rxn-for-chemistry (accessed Jun. 27, 2024).."},{"issue":"1","key":"10.1016\/j.compbiomed.2025.109727_bib66","doi-asserted-by":"crossref","DOI":"10.1038\/s42005-020-0338-y","article-title":"Autonomous molecular design by Monte-Carlo tree search and rapid evaluations using molecular dynamics simulations","volume":"3","author":"Kajita","year":"2020","journal-title":"Commun. Phys."},{"issue":"9","key":"10.1016\/j.compbiomed.2025.109727_bib67","doi-asserted-by":"crossref","DOI":"10.1002\/jcla.24655","article-title":"Antibiotic resistance: the challenges and some emerging strategies for tackling a global menace","volume":"36","author":"Chinemerem Nwobodo","year":"2022","journal-title":"J. Clin. Lab. Anal."},{"key":"10.1016\/j.compbiomed.2025.109727_bib68","series-title":"COMBATING ANTIMICROBIAL RESISTANCE AND PROTECTING THE MIRACLE OF MODERN MEDICINE","author":"Buckley","year":"2022"},{"issue":"1","key":"10.1016\/j.compbiomed.2025.109727_bib69","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.01041-09","article-title":"Attributable hospital cost and length of stay associated with health care-associated infections caused by antibiotic-resistant gram-negative bacteria","volume":"54","author":"Mauldin","year":"2010","journal-title":"Antimicrob. Agents Chemother."},{"issue":"7","key":"10.1016\/j.compbiomed.2025.109727_bib70","doi-asserted-by":"crossref","DOI":"10.1021\/acs.bioconjchem.2c00467","article-title":"Designing new hybrid antibiotics: proline-rich antimicrobial peptides conjugated to the aminoglycoside tobramycin","volume":"34","author":"Gambato","year":"2023","journal-title":"Bioconjugate Chem."},{"key":"10.1016\/j.compbiomed.2025.109727_bib71","article-title":"Methicillin-resistant staphylococcus aureus infection and treatment options","volume":"vol. 2069","author":"Chalmers","year":"2020"},{"issue":"5","key":"10.1016\/j.compbiomed.2025.109727_bib72","doi-asserted-by":"crossref","DOI":"10.3390\/antibiotics11050606","article-title":"Recent developments in methicillin-resistant Staphylococcus aureus (MRSA) treatment: a review","volume":"11","author":"Nandhini","year":"2022","journal-title":"Antibiotics"},{"issue":"5","key":"10.1016\/j.compbiomed.2025.109727_bib73","doi-asserted-by":"crossref","DOI":"10.1111\/cmi.13317","article-title":"Intracellular Staphylococcus aureus and host cell death pathways","volume":"23","author":"Soe","year":"2021","journal-title":"Cell Microbiol."},{"issue":"6","key":"10.1016\/j.compbiomed.2025.109727_bib74","doi-asserted-by":"crossref","DOI":"10.1038\/s41579-023-00852-y","article-title":"Staphylococcus aureus host interactions and adaptation","volume":"21","author":"Howden","year":"2023","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.compbiomed.2025.109727_bib75","doi-asserted-by":"crossref","DOI":"10.3389\/fddsv.2024.1362456","article-title":"Integrative computational approaches for discovery and evaluation of lead compound for drug design","volume":"4","author":"Naithani","year":"2024","journal-title":"Front. Drug Discov."},{"key":"10.1016\/j.compbiomed.2025.109727_bib76","article-title":"Computational resources and chemoinformatics for translational health research","volume":"139","author":"Tripathi","year":"2024","journal-title":"Adv. Protein Chem. Struct. Biol."},{"key":"10.1016\/j.compbiomed.2025.109727_bib77","unstructured":"Pharmacophore - an overview | ScienceDirect Topics.\u201d https:\/\/www.sciencedirect.com\/topics\/immunology-and-microbiology\/pharmacophore (accessed Jul. 01, 2024).."},{"issue":"2","key":"10.1016\/j.compbiomed.2025.109727_bib78","doi-asserted-by":"crossref","DOI":"10.3390\/bios13020258","article-title":"Recent advances on peptide-based biosensors and electronic noses for foodborne pathogen detection","volume":"13","author":"Escobar","year":"2023","journal-title":"Biosensors"},{"issue":"11","key":"10.1016\/j.compbiomed.2025.109727_bib79","doi-asserted-by":"crossref","DOI":"10.1021\/acsinfecdis.2c00406","article-title":"Development of antimicrobial peptide-antibiotic conjugates to improve the outer membrane permeability of antibiotics against gram-negative bacteria","volume":"8","author":"Yamauchi","year":"2022","journal-title":"ACS Infect. Dis."},{"issue":"4","key":"10.1016\/j.compbiomed.2025.109727_bib80","doi-asserted-by":"crossref","DOI":"10.1016\/j.cell.2020.01.021","article-title":"A deep learning approach to antibiotic discovery","volume":"180","author":"Stokes","year":"2020","journal-title":"Cell"},{"issue":"6","key":"10.1016\/j.compbiomed.2025.109727_bib81","doi-asserted-by":"crossref","first-page":"492","DOI":"10.3390\/antibiotics13060492","article-title":"Halicin: a new horizon in antibacterial therapy against veterinary pathogens","volume":"13","author":"Wang","year":"2024","journal-title":"Antibiotics"},{"issue":"6","key":"10.1016\/j.compbiomed.2025.109727_bib82","doi-asserted-by":"crossref","DOI":"10.1021\/acs.jcim.0c00352","article-title":"Machine learning algorithm identifies an antibiotic vocabulary for permeating gram-negative bacteria","volume":"60","author":"Mansbach","year":"2020","journal-title":"J. Chem. Inf. Model."},{"issue":"1","key":"10.1016\/j.compbiomed.2025.109727_bib83","doi-asserted-by":"crossref","DOI":"10.3390\/ijms24010339","article-title":"Ligand-based drug design of novel antimicrobials against Staphylococcus aureus by targeting bacterial transcription","volume":"24","author":"Ye","year":"2023","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.compbiomed.2025.109727_bib84","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2020.00118","article-title":"Pharmacophore-based virtual screening toward the discovery of novel anti-echinococcal compounds","volume":"10","author":"Liu","year":"2020","journal-title":"Front. Cell. Infect. Microbiol."},{"issue":"12","key":"10.1016\/j.compbiomed.2025.109727_bib85","doi-asserted-by":"crossref","DOI":"10.1007\/s00044-015-1445-2","article-title":"Discovery of a potent broad spectrum antimicrobial agent through pharmacophore modeling, virtual screening, in vitro antimicrobial evaluation and gastrointestinal permeation studies","volume":"24","author":"Mishra","year":"2015","journal-title":"Med. Chem. Res."},{"key":"10.1016\/j.compbiomed.2025.109727_bib86","unstructured":"\u201cAdenosine Triphosphatase Inhibitor - an overview | ScienceDirect Topics.\u201d https:\/\/www.sciencedirect.com\/topics\/medicine-and-dentistry\/adenosine-triphosphatase-inhibitor (accessed Jul. 01, 2024).."},{"issue":"4","key":"10.1016\/j.compbiomed.2025.109727_bib87","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1021\/acsinfecdis.4c00128","article-title":"Gyrase and topoisomerase IV: recycling old targets for new antibacterials to combat fluoroquinolone resistance","volume":"10","author":"Collins","year":"2024","journal-title":"ACS Infect. Dis."},{"issue":"15","key":"10.1016\/j.compbiomed.2025.109727_bib88","doi-asserted-by":"crossref","DOI":"10.1002\/cam4.70074","article-title":"Structure\u2010based pharmacophore modeling for precision inhibition of mutant ESR2 in breast cancer: a systematic computational approach","volume":"13","author":"Islam","year":"2024","journal-title":"Cancer Med."},{"key":"10.1016\/j.compbiomed.2025.109727_bib89","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.drudis.2010.03.013","article-title":"Pharmacophore modeling and applications in drug discovery: challenges and recent advances","volume":"15","author":"Yang","year":"2010","journal-title":"Drug Discov. Today"},{"issue":"16","key":"10.1016\/j.compbiomed.2025.109727_bib90","doi-asserted-by":"crossref","DOI":"10.1039\/D0RA10168K","article-title":"Ligand-based pharmacophore modeling, virtual screening and biological evaluation to identify novel TGR5 agonists","volume":"11","author":"Zhao","year":"2021","journal-title":"RSC Adv."},{"issue":"5","key":"10.1016\/j.compbiomed.2025.109727_bib91","doi-asserted-by":"crossref","DOI":"10.1177\/24725552211000669","article-title":"A perspective on synthetic biology in drug discovery and development\u2014current impact and future opportunities","volume":"26","author":"David","year":"2021","journal-title":"SLAS Discovery"},{"key":"10.1016\/j.compbiomed.2025.109727_bib92","series-title":"Therapeutical Chemistry","article-title":"Lipinski's rule of five","author":"Barret","year":"2018"},{"key":"10.1016\/j.compbiomed.2025.109727_bib93","series-title":"In xPharm: the Comprehensive Pharmacology Reference","article-title":"Ciprofloxacin","author":"Doble","year":"2007"},{"issue":"FEB","key":"10.1016\/j.compbiomed.2025.109727_bib94","article-title":"Embracing the diversity of halogen bonding motifs in fragment-based drug discovery-construction of a diversity-optimized halogen-enriched fragment library","volume":"7","author":"Heidrich","year":"2019","journal-title":"Front. Chem."},{"issue":"21","key":"10.1016\/j.compbiomed.2025.109727_bib95","doi-asserted-by":"crossref","DOI":"10.1021\/acs.jmedchem.8b01453","article-title":"Halogens in protein-ligand binding mechanism: a structural perspective","volume":"62","author":"Shinada","year":"2019","journal-title":"J. Med. Chem."},{"issue":"6","key":"10.1016\/j.compbiomed.2025.109727_bib96","doi-asserted-by":"crossref","DOI":"10.1021\/acs.jcim.0c00032","article-title":"Interaction nature and computational methods for halogen bonding: a perspective","volume":"60","author":"Zhu","year":"2020","journal-title":"J. Chem. Inf. Model."},{"issue":"6","key":"10.1016\/j.compbiomed.2025.109727_bib97","doi-asserted-by":"crossref","DOI":"10.1021\/acs.jmedchem.1c01854","article-title":"Halogen bonds exist between noncovalent ligands and natural nucleic acids","volume":"65","author":"Mu","year":"2022","journal-title":"J. Med. Chem."},{"key":"10.1016\/j.compbiomed.2025.109727_bib98","doi-asserted-by":"crossref","DOI":"10.1016\/j.ccr.2020.213281","article-title":"Halogen bonding motifs for anion recognition","volume":"416","author":"Pancholi","year":"2020","journal-title":"Coord. Chem. Rev."},{"issue":"1","key":"10.1016\/j.compbiomed.2025.109727_bib99","doi-asserted-by":"crossref","DOI":"10.1002\/wcms.1694","article-title":"Recent advances in deep learning for retrosynthesis","volume":"14","author":"Zhong","year":"2024","journal-title":"Wiley Interdiscip. Rev. Comput. Mol. Sci."}],"container-title":["Computers in Biology and Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0010482525000770?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0010482525000770?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T09:34:32Z","timestamp":1774344872000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0010482525000770"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3]]},"references-count":99,"alternative-id":["S0010482525000770"],"URL":"https:\/\/doi.org\/10.1016\/j.compbiomed.2025.109727","relation":{},"ISSN":["0010-4825"],"issn-type":[{"value":"0010-4825","type":"print"}],"subject":[],"published":{"date-parts":[[2025,3]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Pharmacophore-guided computational modeling of quinolone-ATPase conjugate inhibitors targeting DNA GyrB subunit of Staphylococcus aureus","name":"articletitle","label":"Article Title"},{"value":"Computers in Biology and Medicine","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.compbiomed.2025.109727","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 Elsevier Ltd. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}],"article-number":"109727"}}