{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T00:47:47Z","timestamp":1778201267582,"version":"3.51.4"},"reference-count":193,"publisher":"Springer Science and Business Media LLC","issue":"4-6","license":[{"start":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T00:00:00Z","timestamp":1758844800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T00:00:00Z","timestamp":1758844800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"name":"Chiang Mai University and Center of Excellence for Innovation in Chemistry. Partially supported by CMU Proactive Researcher Scheme (2024), Chiang Mai University","award":["Fundamental Fund 2025"],"award-info":[{"award-number":["Fundamental Fund 2025"]}]},{"name":"Chiang Mai University and Center of Excellence for Innovation in Chemistry. Partially supported by CMU Proactive Researcher Scheme (2024), Chiang Mai University","award":["Fundamental Fund 2025"],"award-info":[{"award-number":["Fundamental Fund 2025"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Biol Cybern"],"DOI":"10.1007\/s00422-025-01026-0","type":"journal-article","created":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T06:02:45Z","timestamp":1758866565000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Molecular dynamics simulations of proteins: an in-depth review of computational strategies, structural insights, and their role in medicinal chemistry and drug development"],"prefix":"10.1007","volume":"119","author":[{"given":"Bita","family":"Farhadi","sequence":"first","affiliation":[]},{"given":"Mahnoush","family":"Beygisangchin","sequence":"additional","affiliation":[]},{"given":"Nakisa","family":"Ghamari","sequence":"additional","affiliation":[]},{"given":"Jaroon","family":"Jakmunee","sequence":"additional","affiliation":[]},{"given":"Tang","family":"Tang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,9,26]]},"reference":[{"issue":"1","key":"1026_CR1","doi-asserted-by":"publisher","first-page":"13398","DOI":"10.1038\/s41598-023-40160-2","volume":"13","author":"PC Agu","year":"2023","unstructured":"Agu PC et al (2023) Molecular Docking as a tool for the discovery of molecular targets of nutraceuticals in diseases management. Sci Rep 13(1):13398","journal-title":"Sci Rep"},{"key":"1026_CR2","doi-asserted-by":"crossref","unstructured":"Ahmad A (2019) Breast cancer statistics: recent trends. Breast cancer metastasis and drug resistance: challenges and progress, : pp. 1\u20137","DOI":"10.1007\/978-3-030-20301-6_1"},{"key":"1026_CR3","doi-asserted-by":"crossref","unstructured":"Ahmad B et al (2022) Identification of natural marine compounds as potential inhibitors of CDK2 using molecular Docking and molecular dynamics simulation approach. J Biomol Struct Dynamics, : p. 1\u201311","DOI":"10.1080\/07391102.2022.2135594"},{"issue":"17","key":"1026_CR4","doi-asserted-by":"publisher","first-page":"8506","DOI":"10.1080\/07391102.2022.2135594","volume":"41","author":"B Ahmad","year":"2023","unstructured":"Ahmad B (2023) Identification of natural marine compounds as potential inhibitors of CDK2 using molecular docking and molecular dynamics simulation approach. J Biomol Struct Dyn 41(17):8506\u20138516","journal-title":"J Biomol Struct Dyn"},{"key":"1026_CR5","doi-asserted-by":"publisher","first-page":"7","DOI":"10.53388\/MDM202508008","volume":"8","author":"S Ahmad","year":"2025","unstructured":"Ahmad S, Bano N, Raza K (2025) RCSB protein data bank: revolutionising drug discovery and design for over five decades. Med Data Min 8:7\u201311","journal-title":"Med Data Min"},{"key":"1026_CR6","doi-asserted-by":"crossref","unstructured":"Alhmoud JF et al (2021) DNA damage\/repair management in cancers. Advances in Medical Biochemistry, Genomics, Physiology, and Pathology, : pp. 309\u2013339","DOI":"10.1201\/9781003180449-12"},{"key":"1026_CR7","doi-asserted-by":"publisher","first-page":"101251","DOI":"10.1016\/j.imu.2023.101251","volume":"39","author":"KS Andalib","year":"2023","unstructured":"Andalib KS et al (2023a) Identification of novel MCM2 inhibitors from catharanthus roseus by pharmacoinformatics, molecular Docking and molecular dynamics simulation-based evaluation. Inf Med Unlocked 39:101251","journal-title":"Inf Med Unlocked"},{"key":"1026_CR8","doi-asserted-by":"crossref","unstructured":"Andalib KS et al (2023b) Identification of novel MCM2 inhibitors from catharanthus roseus by pharmacoinformatics, molecular Docking and molecular dynamics simulation-based evaluation. Inf Med Unlocked, : p. 101251","DOI":"10.1016\/j.imu.2023.101251"},{"issue":"4096","key":"1026_CR9","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1126\/science.181.4096.223","volume":"181","author":"CB Anfinsen","year":"1973","unstructured":"Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181(4096):223\u2013230","journal-title":"Science"},{"issue":"1","key":"1026_CR10","doi-asserted-by":"publisher","first-page":"4742","DOI":"10.1038\/s41598-022-08359-x","volume":"12","author":"JMC Ar\u00e9valo","year":"2022","unstructured":"Ar\u00e9valo JMC, Amorim JC (2022) Virtual screening, optimization and molecular dynamics analyses highlighting a Pyrrolo [1, 2-a] Quinazoline derivative as a potential inhibitor of DNA gyrase B of Mycobacterium tuberculosis. Sci Rep 12(1):4742","journal-title":"Sci Rep"},{"key":"1026_CR11","doi-asserted-by":"publisher","first-page":"109119","DOI":"10.1016\/j.foodcont.2022.109119","volume":"140","author":"B Arulrajah","year":"2022","unstructured":"Arulrajah B et al (2022) Antibacterial and antifungal activity of Kenaf seed peptides and their effect on Microbiological safety and physicochemical properties of some food models. Food Control 140:109119","journal-title":"Food Control"},{"key":"1026_CR12","doi-asserted-by":"publisher","first-page":"114757","DOI":"10.1016\/j.lwt.2023.114757","volume":"181","author":"B Arulrajah","year":"2023","unstructured":"Arulrajah B et al (2023a) Elucidating the mechanisms underlying the action of Kenaf seed peptides mixture against gram-positive and gram-negative bacteria and its efficacy in whole milk preservation. Lwt 181:114757","journal-title":"Lwt"},{"key":"1026_CR13","doi-asserted-by":"crossref","unstructured":"Arulrajah B et al (2023b) Elucidating the mechanisms underlying the action of kenaf seed peptides mixture against gram-positive and gram-negative bacteria and its efficacy in whole milk preservation. LWT, : p. 114757","DOI":"10.1016\/j.lwt.2023.114757"},{"issue":"18","key":"1026_CR14","doi-asserted-by":"publisher","first-page":"1563","DOI":"10.1080\/08927022.2019.1662003","volume":"45","author":"F Azam","year":"2019","unstructured":"Azam F (2019) Rutin as promising drug for the treatment of Parkinson\u2019s disease: an assessment of MAO-B inhibitory potential by docking, molecular dynamics and DFT studies. Mol Simul 45(18):1563\u20131571","journal-title":"Mol Simul"},{"issue":"3","key":"1026_CR15","doi-asserted-by":"publisher","DOI":"10.1002\/wcms.1581","volume":"12","author":"Q Bai","year":"2022","unstructured":"Bai Q et al (2022) Application advances of deep learning methods for de novo drug design and molecular dynamics simulation. WIREs Comput Mol Sci 12(3):e1581","journal-title":"WIREs Comput Mol Sci"},{"issue":"3","key":"1026_CR16","doi-asserted-by":"publisher","first-page":"804","DOI":"10.1016\/j.drudis.2020.12.005","volume":"26","author":"R Banerjee","year":"2021","unstructured":"Banerjee R, Perera L, Tillekeratne LV (2021) Potential SARS-CoV-2 main protease inhibitors. Drug Discov Today 26(3):804\u2013816","journal-title":"Drug Discov Today"},{"key":"1026_CR17","doi-asserted-by":"crossref","unstructured":"Banerjee J et al (2025) Signaling molecules: importance in health and disease Conditions, in Neuroreceptor endocytosis and signaling in health and disease. Springer, pp 19\u201360","DOI":"10.1007\/978-3-031-81991-9_2"},{"issue":"19","key":"1026_CR18","doi-asserted-by":"publisher","first-page":"1813","DOI":"10.1056\/NEJMoa2007764","volume":"383","author":"JH Beigel","year":"2020","unstructured":"Beigel JH et al (2020) Remdesivir for the treatment of Covid-19. N Engl J Med 383(19):1813\u20131826","journal-title":"N Engl J Med"},{"issue":"10","key":"1026_CR19","doi-asserted-by":"publisher","first-page":"4799","DOI":"10.1038\/s41596-021-00597-z","volume":"16","author":"BJ Bender","year":"2021","unstructured":"Bender BJ et al (2021) A practical guide to large-scale Docking. Nat Protoc 16(10):4799\u20134832","journal-title":"Nat Protoc"},{"key":"1026_CR20","doi-asserted-by":"publisher","DOI":"10.1017\/S0033583525000034","volume":"58","author":"HM Berman","year":"2025","unstructured":"Berman HM, Burley SK (2025) Protein data bank (PDB): fifty-three years young and having a transformative impact on science and society. Q Rev Biophys 58:e9","journal-title":"Q Rev Biophys"},{"issue":"1","key":"1026_CR21","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM (2000) The protein data bank. Nucleic Acids Res 28(1):235\u2013242","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"1026_CR22","doi-asserted-by":"publisher","first-page":"492","DOI":"10.1021\/cb100410m","volume":"6","author":"S Betzi","year":"2011","unstructured":"Betzi S et al (2011) Discovery of a potential allosteric ligand binding site in CDK2. ACS Chem Biol 6(5):492\u2013501","journal-title":"ACS Chem Biol"},{"issue":"15","key":"1026_CR23","doi-asserted-by":"publisher","first-page":"3598","DOI":"10.1021\/acs.jpcb.4c00519","volume":"128","author":"H Bian","year":"2024","unstructured":"Bian H et al (2024) Understanding the reversible binding of a multichain protein\u2013protein complex through free-energy calculations. J Phys Chem B 128(15):3598\u20133604","journal-title":"J Phys Chem B"},{"key":"1026_CR24","doi-asserted-by":"publisher","DOI":"10.3389\/fchem.2020.00107","volume":"8","author":"M Bissaro","year":"2020","unstructured":"Bissaro M, Sturlese M, Moro S (2020) Exploring the RNA-recognition mechanism using supervised molecular dynamics (SuMD) simulations: toward a rational design for ribonucleic-targeting molecules? Front Chem 8:107","journal-title":"Front Chem"},{"key":"1026_CR25","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1002\/9783527840748.ch7","volume":"1","author":"O Borbulevych","year":"2024","unstructured":"Borbulevych O, Westerhoff LM (2024) Recent advances in practical quantum mechanics and M ixed-QM\/MM\u2010Driven X\u2010Ray crystallography and cryogenic electron microscopy (Cryo\u2010EM) and their impact on Structure\u2010Based drug discovery. Comput Drug Discovery: Methods Appl 1:157\u2013182","journal-title":"Comput Drug Discovery: Methods Appl"},{"issue":"6","key":"1026_CR26","doi-asserted-by":"publisher","first-page":"1340","DOI":"10.3390\/molecules25061340","volume":"25","author":"Z Breijyeh","year":"2020","unstructured":"Breijyeh Z, Jubeh B, Karaman R (2020) Resistance of gram-negative bacteria to current antibacterial agents and approaches to resolve it. Molecules 25(6):1340","journal-title":"Molecules"},{"key":"1026_CR27","unstructured":"Brooks CL (1987) Computer simulation of liquids: By MP Allen (University of Bristol) and DJ Tildesley (Southampton University). Clarendon Press, Oxford, UK; Oxford University Press, New York; xix\u2009+\u2009385 pp. ISBN 0470-20812-0. 1989, Springer"},{"key":"1026_CR28","doi-asserted-by":"publisher","DOI":"10.1063\/1.2810459","author":"CL Brooks","year":"1990","unstructured":"Brooks CL ((1990)) Proteins: a theoretical perspective of dynamics, structure and thermodynamics. Phys Today. https:\/\/doi.org\/10.1063\/1.2810459","journal-title":"Phys Today"},{"issue":"7910","key":"1026_CR29","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1038\/s41586-022-04654-9","volume":"605","author":"L Cao","year":"2022","unstructured":"Cao L et al (2022) Design of protein-binding proteins from the target structure alone. Nature 605(7910):551\u2013560","journal-title":"Nature"},{"issue":"10","key":"1026_CR30","doi-asserted-by":"publisher","first-page":"2219","DOI":"10.1021\/acs.jpcb.3c04823","volume":"128","author":"M Caparotta","year":"2024","unstructured":"Caparotta M, Perez A (2024) Advancing molecular dynamics: toward standardization, integration, and data accessibility in structural biology. J Phys Chem B 128(10):2219\u20132227","journal-title":"J Phys Chem B"},{"issue":"1","key":"1026_CR31","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1093\/protein\/gzl051","volume":"20","author":"O Carugo","year":"2007","unstructured":"Carugo O (2007) Statistical validation of the root-mean-square-distance, a measure of protein structural proximity. Protein Eng Des Sel 20(1):33\u201337","journal-title":"Protein Eng Des Sel"},{"issue":"17","key":"1026_CR32","doi-asserted-by":"publisher","first-page":"6880","DOI":"10.1021\/acs.jcim.4c01174","volume":"64","author":"J Chen","year":"2024","unstructured":"Chen J et al (2024) Conformations of KRAS4B affected by its partner binding and G12C mutation: insights from GaMD trajectory-image transformation-based deep learning. J Chem Inf Model 64(17):6880\u20136898","journal-title":"J Chem Inf Model"},{"issue":"8","key":"1026_CR33","doi-asserted-by":"publisher","first-page":"4189","DOI":"10.1021\/acs.jcim.5c00096","volume":"65","author":"J Chen","year":"2025","unstructured":"Chen J (2025) Activity regulation and conformation response of Janus kinase 3 mediated by phosphorylation: exploration from correlation network analysis and Markov model. J Chem Inf Model 65(8):4189\u20134205","journal-title":"J Chem Inf Model"},{"issue":"2","key":"1026_CR34","doi-asserted-by":"publisher","first-page":"237","DOI":"10.2174\/0929867321666141106113633","volume":"22","author":"TA Chohan","year":"2014","unstructured":"Chohan TA (2014) Cyclin-dependent kinase-2 as a target for cancer therapy: progress in the development of CDK2 inhibitors as anti-cancer agents. Curr Med Chem 22(2):237\u2013263","journal-title":"Curr Med Chem"},{"issue":"7","key":"1026_CR35","doi-asserted-by":"publisher","first-page":"e0235030","DOI":"10.1371\/journal.pone.0235030","volume":"15","author":"MI Choudhary","year":"2020","unstructured":"Choudhary MI et al (2020) In silico identification of potential inhibitors of key SARS-CoV-2 3CL hydrolase (Mpro) via molecular docking, MMGBSA predictive binding energy calculations, and molecular dynamics simulation. PLoS ONE 15(7):e0235030","journal-title":"PLoS ONE"},{"issue":"1","key":"1026_CR36","doi-asserted-by":"publisher","DOI":"10.1002\/wcms.1689","volume":"14","author":"MG Costa","year":"2024","unstructured":"Costa MG et al (2024) Computational biophysics meets cryo-EM revolution in the search for the functional dynamics of biomolecular systems. WIREs Comput Mol Sci 14(1):e1689","journal-title":"WIREs Comput Mol Sci"},{"issue":"35","key":"1026_CR37","doi-asserted-by":"publisher","first-page":"355401","DOI":"10.1088\/1361-6463\/aad4ec","volume":"51","author":"J Cui","year":"2018","unstructured":"Cui J et al (2018) Molecular dynamics simulation of S. cerevisiae glucan destruction by plasma ROS based on ReaxFF. J Phys D 51(35):355401","journal-title":"J Phys D"},{"issue":"5","key":"1026_CR38","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1016\/j.jshs.2020.01.004","volume":"9","author":"A De la Rosa","year":"2020","unstructured":"De la Rosa A et al (2020) Physical exercise in the prevention and treatment of Alzheimer\u2019s disease. J Sport Health Sci 9(5):394\u2013404","journal-title":"J Sport Health Sci"},{"issue":"9","key":"1026_CR39","doi-asserted-by":"publisher","first-page":"4035","DOI":"10.1021\/acs.jmedchem.5b01684","volume":"59","author":"M De Vivo","year":"2016","unstructured":"De Vivo M et al (2016) Role of molecular dynamics and related methods in drug discovery. J Med Chem 59(9):4035\u20134061","journal-title":"J Med Chem"},{"key":"1026_CR40","doi-asserted-by":"publisher","DOI":"10.1016\/j.imu.2023.101252","volume":"39","author":"K Deepasree","year":"2023","unstructured":"Deepasree K, Subhashree V (2023) Molecular docking and dynamic simulation studies of terpenoid compounds against phosphatidylinositol-specific phospholipase C from Listeria monocytogenes. Inf Med Unlocked 39:101252","journal-title":"Inf Med Unlocked"},{"key":"1026_CR41","doi-asserted-by":"crossref","unstructured":"Deepasree K, Venugopal S (2023) Molecular Docking and dynamic simulation studies of terpenoid compounds against phosphatidylinositol-specific phospholipase C from Listeria monocytogenes. Inf Med Unlocked, : p. 101252","DOI":"10.1016\/j.imu.2023.101252"},{"issue":"1","key":"1026_CR42","doi-asserted-by":"publisher","DOI":"10.5455\/javar.2021.h481","volume":"8","author":"D Dey","year":"2021","unstructured":"Dey D et al (2021) Molecular optimization, docking, and dynamic simulation profiling of selective aromatic phytochemical ligands in blocking the SARS-CoV-2 S protein attachment to ACE2 receptor: an in silico approach of targeted drug designing. J Adv Vet Anim Res 8(1):24","journal-title":"J Adv Vet Anim Res"},{"issue":"2","key":"1026_CR43","doi-asserted-by":"publisher","first-page":"917","DOI":"10.1007\/s11831-022-09821-9","volume":"30","author":"A Dhillon","year":"2023","unstructured":"Dhillon A, Singh A, Bhalla VK (2023) A systematic review on biomarker identification for cancer diagnosis and prognosis in multi-omics: from computational needs to machine learning and deep learning. Arch Comput Methods Eng 30(2):917\u2013949","journal-title":"Arch Comput Methods Eng"},{"issue":"10","key":"1026_CR44","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.70093","volume":"46","author":"L Dong","year":"2025","unstructured":"Dong L, Li P, Wang B (2025) Enhancing MM\/P (G) BSA methods: integration of formulaic entropy for improved binding free energy calculations. J Comput Chem 46(10):e70093","journal-title":"J Comput Chem"},{"issue":"2","key":"1026_CR45","doi-asserted-by":"publisher","DOI":"10.3390\/ijms17020144","volume":"17","author":"X Du","year":"2016","unstructured":"Du X et al (2016) Insights into protein\u2013ligand interactions: mechanisms, models, and methods. Int J Mol Sci 17(2):144","journal-title":"Int J Mol Sci"},{"key":"1026_CR46","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1741-7007-9-71","volume":"9","author":"JD Durrant","year":"2011","unstructured":"Durrant JD, McCammon JA (2011) Molecular dynamics simulations and drug discovery. BMC Biol 9:1\u20139","journal-title":"BMC Biol"},{"issue":"16","key":"1026_CR47","doi-asserted-by":"publisher","first-page":"2755","DOI":"10.2174\/13816128113199990567","volume":"20","author":"S Ebihara","year":"2014","unstructured":"Ebihara S et al (2014) Thermal taste and anti-aspiration drugs: a novel drug discovery against pneumonia. Curr Pharm Des 20(16):2755\u20132759","journal-title":"Curr Pharm Des"},{"issue":"5","key":"1026_CR48","doi-asserted-by":"publisher","DOI":"10.3390\/life14050630","volume":"14","author":"M Eigenfeld","year":"2024","unstructured":"Eigenfeld M, Lupp KF, Schwaminger SP (2024) Role of natural binding proteins in therapy and diagnostics. Life 14(5):630","journal-title":"Life"},{"issue":"1","key":"1026_CR49","doi-asserted-by":"publisher","first-page":"6241017","DOI":"10.1155\/2018\/6241017","volume":"2018","author":"AB Enogieru","year":"2018","unstructured":"Enogieru AB et al (2018) Rutin as a potent antioxidant: implications for neurodegenerative disorders. Oxidative Med Cell Longev 2018(1):6241017","journal-title":"Oxidative Med Cell Longev"},{"key":"1026_CR50","doi-asserted-by":"crossref","unstructured":"Epstein CJ, Goldberger RF, Anfinsen CB (1963) The genetic control of tertiary protein structure: studies with model systems. Cold spring harbor symposia on quantitative biology. Cold Spring Harbor Laboratory Press","DOI":"10.1101\/SQB.1963.028.01.060"},{"issue":"4","key":"1026_CR51","doi-asserted-by":"publisher","first-page":"1625","DOI":"10.1093\/nar\/gkad013","volume":"51","author":"R Esmaeeli","year":"2023","unstructured":"Esmaeeli R, Bauz\u00e1 A, Perez A (2023) Structural predictions of protein\u2013DNA binding: MELD-DNA. Nucleic Acids Res 51(4):1625\u20131636","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"1026_CR52","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1038\/nrn3901","volume":"16","author":"A Fornito","year":"2015","unstructured":"Fornito A, Zalesky A, Breakspear M (2015) The connectomics of brain disorders. Nat Rev Neurosci 16(3):159\u2013172","journal-title":"Nat Rev Neurosci"},{"issue":"4","key":"1026_CR53","doi-asserted-by":"publisher","first-page":"1114","DOI":"10.1038\/s41596-021-00676-1","volume":"17","author":"H Fu","year":"2022","unstructured":"Fu H et al (2022) Accurate determination of protein: ligand standard binding free energies from molecular dynamics simulations. Nat Protoc 17(4):1114\u20131141","journal-title":"Nat Protoc"},{"issue":"24","key":"1026_CR54","doi-asserted-by":"publisher","first-page":"7791","DOI":"10.1021\/acs.jcim.3c01107","volume":"63","author":"JJ Galano-Frutos","year":"2023","unstructured":"Galano-Frutos JJ, Ner\u00edn-Fonz F, Sancho J (2023) Calculation of protein folding thermodynamics using molecular dynamics simulations. J Chem Inf Model 63(24):7791\u20137806","journal-title":"J Chem Inf Model"},{"key":"1026_CR55","first-page":"527","volume":"23","author":"R Galindo-Murillo","year":"2021","unstructured":"Galindo-Murillo R, Cohen JS, Akabayov B (2021) Molecular dynamics simulations of acyclic analogs of nucleic acids for antisense inhibition. Mol Ther 23:527\u2013535","journal-title":"Mol Ther"},{"issue":"2","key":"1026_CR56","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1016\/j.jsps.2016.04.025","volume":"25","author":"A Ganeshpurkar","year":"2017","unstructured":"Ganeshpurkar A, Saluja AK (2017) The pharmacological potential of Rutin. Saudi Pharm J 25(2):149\u2013164","journal-title":"Saudi Pharm J"},{"issue":"8","key":"1026_CR57","doi-asserted-by":"publisher","first-page":"474","DOI":"10.1038\/s41580-019-0136-0","volume":"20","author":"LR Ganser","year":"2019","unstructured":"Ganser LR et al (2019) The roles of structural dynamics in the cellular functions of RNAs. Nat Rev Mol Cell Biol 20(8):474\u2013489","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"1","key":"1026_CR58","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1093\/bioinformatics\/btab616","volume":"38","author":"J Gao","year":"2022","unstructured":"Gao J et al (2022) Precise estimation of residue relative solvent accessible area from C\u03b1 atom distance matrix using a deep learning method. Bioinformatics 38(1):94\u201398","journal-title":"Bioinformatics"},{"issue":"16","key":"1026_CR59","doi-asserted-by":"publisher","first-page":"17691","DOI":"10.1021\/acsomega.4c01309","volume":"9","author":"M Garbagnoli","year":"2024","unstructured":"Garbagnoli M et al (2024) Biophysical assays for investigating modulators of macromolecular complexes: an overview. ACS Omega 9(16):17691\u201317705","journal-title":"ACS Omega"},{"key":"1026_CR60","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/j.pbiomolbio.2023.08.002","volume":"185","author":"E Gayathiri","year":"2023","unstructured":"Gayathiri E et al (2023) Computational approaches for modeling and structural design of biological systems: a comprehensive review. Prog Biophys Mol Biol 185:17\u201332","journal-title":"Prog Biophys Mol Biol"},{"key":"1026_CR61","doi-asserted-by":"publisher","first-page":"1162","DOI":"10.1016\/j.csbj.2019.07.010","volume":"17","author":"H Geng","year":"2019","unstructured":"Geng H et al (2019) Applications of molecular dynamics simulation in structure prediction of peptides and proteins. Comput Struct Biotechnol J 17:1162\u20131170","journal-title":"Comput Struct Biotechnol J"},{"issue":"1","key":"1026_CR62","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1074\/jbc.REV119.006794","volume":"295","author":"A Gershenson","year":"2020","unstructured":"Gershenson A et al (2020) Successes and challenges in simulating the folding of large proteins. J Biol Chem 295(1):15\u201333","journal-title":"J Biol Chem"},{"issue":"1","key":"1026_CR63","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1038\/s41597-022-01261-1","volume":"9","author":"S Gervasoni","year":"2022","unstructured":"Gervasoni S et al (2022) AB-DB: Force-Field parameters, MD trajectories, QM-based data, and descriptors of antimicrobials. Sci Data 9(1):148","journal-title":"Sci Data"},{"issue":"1","key":"1026_CR64","first-page":"83","volume":"6","author":"B Ghalami-Choobar","year":"2018","unstructured":"Ghalami-Choobar B, Moghadam H (2018) Molecular docking based on virtual screening, molecular dynamics and atoms in molecules studies to identify the potential human epidermal receptor 2 intracellular domain inhibitors. Phys Chem Res 6(1):83\u2013103","journal-title":"Phys Chem Res"},{"issue":"12","key":"1026_CR65","doi-asserted-by":"publisher","first-page":"4362","DOI":"10.1080\/07391102.2020.1779818","volume":"39","author":"R Ghosh","year":"2021","unstructured":"Ghosh R et al ((2021)) Evaluation of green tea polyphenols as novel Corona virus (SARS CoV-2) main protease (Mpro) inhibitors\u2013an in silico docking and molecular dynamics simulation study. J Biomol Struct Dyn 39(12):4362\u20134374","journal-title":"J Biomol Struct Dyn"},{"issue":"3","key":"1026_CR66","doi-asserted-by":"publisher","first-page":"1963","DOI":"10.1007\/s11030-021-10211-9","volume":"25","author":"B Gogoi","year":"2021","unstructured":"Gogoi B et al (2021a) Identification of potential plant-based inhibitor against viral proteases of SARS-CoV-2 through molecular docking, MM-PBSA binding energy calculations and molecular dynamics simulation. Mol Divers 25(3):1963\u20131977","journal-title":"Mol Divers"},{"key":"1026_CR67","doi-asserted-by":"publisher","first-page":"1963","DOI":"10.1007\/s11030-021-10211-9","volume":"25","author":"B Gogoi","year":"2021","unstructured":"Gogoi B (2021) Identification of potential plant-based inhibitor against viral proteases of SARS-CoV-2 through molecular docking, MM-PBSA binding energy calculations and molecular dynamics simulation. Mol Divers 25:1963\u20131977","journal-title":"Mol Divers"},{"issue":"5","key":"1026_CR68","doi-asserted-by":"publisher","first-page":"1331","DOI":"10.1002\/1097-0142(20010901)92:5<1331::AID-CNCR1455>3.0.CO;2-M","volume":"92","author":"NS Goldstein","year":"2001","unstructured":"Goldstein NS, Armin M (2001) Epidermal growth factor receptor immunohistochemical reactivity in patients with American Joint Committee on Cancer stage IV colon adenocarcinoma: implications for a standardized scoring system. Cancer 92(5):1331\u20131346","journal-title":"Cancer"},{"key":"1026_CR69","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1051\/sfn\/201112009","volume":"12","author":"MA Gonz\u00e1lez","year":"2011","unstructured":"Gonz\u00e1lez MA (2011) Force fields and molecular dynamics simulations. \u00c9cole th\u00e9matique De La Soci\u00e9t\u00e9 Fran\u00e7aise De La Neutronique 12:169\u2013200","journal-title":"\u00c9cole th\u00e9matique De La Soci\u00e9t\u00e9 Fran\u00e7aise De La Neutronique"},{"key":"1026_CR70","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejmech.2020.112957","volume":"210","author":"M Gozari","year":"2021","unstructured":"Gozari M et al (2021) Chemistry, biosynthesis and biological activity of terpenoids and meroterpenoids in bacteria and fungi isolated from different marine habitats. Eur J Med Chem 210:112957","journal-title":"Eur J Med Chem"},{"issue":"7","key":"1026_CR71","doi-asserted-by":"publisher","first-page":"3932","DOI":"10.1021\/acs.chemrev.3c00550","volume":"124","author":"G Grassmann","year":"2024","unstructured":"Grassmann G et al (2024) Computational approaches to predict protein\u2013protein interactions in crowded cellular environments. Chem Rev 124(7):3932\u20133977","journal-title":"Chem Rev"},{"issue":"23","key":"1026_CR72","doi-asserted-by":"publisher","first-page":"7281","DOI":"10.1021\/ja0319994","volume":"126","author":"A Grishaev","year":"2004","unstructured":"Grishaev A, Bax A (2004) An empirical backbone\u2009\u2013\u2009backbone hydrogen-bonding potential in proteins and its applications to NMR structure refinement and validation. J Am Chem Soc 126(23):7281\u20137292","journal-title":"J Am Chem Soc"},{"issue":"2","key":"1026_CR73","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbad008","volume":"24","author":"S Gu","year":"2023","unstructured":"Gu S (2023) Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning? Brief Bioinform 24(2):bbad008","journal-title":"Brief Bioinform"},{"issue":"4","key":"1026_CR74","doi-asserted-by":"publisher","first-page":"2189","DOI":"10.1021\/acs.jcim.0c00057","volume":"60","author":"H Guterres","year":"2020","unstructured":"Guterres H, Im W (2020) Improving protein-ligand Docking results with high-throughput molecular dynamics simulations. J Chem Inf Model 60(4):2189\u20132198","journal-title":"J Chem Inf Model"},{"issue":"5","key":"1026_CR75","doi-asserted-by":"publisher","first-page":"1645","DOI":"10.1007\/s11224-022-01996-y","volume":"33","author":"AH Hasan","year":"2022","unstructured":"Hasan AH et al (2022) In silico discovery of multi-targeting inhibitors for the COVID-19 treatment by molecular docking, molecular dynamics simulation studies, and ADMET predictions. Struct Chem 33(5):1645\u20131665","journal-title":"Struct Chem"},{"issue":"1","key":"1026_CR76","doi-asserted-by":"publisher","first-page":"67","DOI":"10.4103\/1735-5362.363597","volume":"18","author":"S Hatami","year":"2023","unstructured":"Hatami S et al (2023) Preparing a database of corrected protein structures important in cell signaling pathways. Res Pharm Sci 18(1):67\u201378","journal-title":"Res Pharm Sci"},{"key":"1026_CR77","unstructured":"He X (2025) Machine learning interatomic potentials in biomolecular modeling: principles, architectures, and applications. Biophys Rev, : p. 1\u201313"},{"issue":"6","key":"1026_CR78","doi-asserted-by":"publisher","first-page":"1129","DOI":"10.1016\/j.neuron.2018.08.011","volume":"99","author":"SA Hollingsworth","year":"2018","unstructured":"Hollingsworth SA, Dror RO (2018) Molecular dynamics simulation for all. Neuron 99(6):1129\u20131143","journal-title":"Neuron"},{"issue":"3","key":"1026_CR79","doi-asserted-by":"publisher","first-page":"243","DOI":"10.4161\/viru.19700","volume":"3","author":"A Howard","year":"2012","unstructured":"Howard A et al (2012) Acinetobacter baumannii: an emerging opportunistic pathogen. Virulence 3(3):243\u2013250","journal-title":"Virulence"},{"key":"1026_CR80","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2025.108416","author":"J Howe","year":"2025","unstructured":"Howe J, Barbar EJ (2025) Dynamic interactions of dimeric hub proteins underlie their diverse functions and structures: a comparative analysis of 14-3-3 and LC8. J Biol Chem. https:\/\/doi.org\/10.1016\/j.jbc.2025.108416","journal-title":"J Biol Chem"},{"key":"1026_CR81","doi-asserted-by":"publisher","DOI":"10.1016\/j.foodchem.2022.134824","volume":"405","author":"X Hu","year":"2023","unstructured":"Hu X (2023) Molecular dynamics simulation of the interaction of food proteins with small molecules. Food Chem 405:134824","journal-title":"Food Chem"},{"issue":"7565","key":"1026_CR82","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1038\/nature14886","volume":"524","author":"W Huang","year":"2015","unstructured":"Huang W et al (2015) Structural insights into \u00b5-opioid receptor activation. Nature 524(7565):315\u2013321","journal-title":"Nature"},{"issue":"9","key":"1026_CR83","doi-asserted-by":"publisher","DOI":"10.3390\/ph14090937","volume":"14","author":"D Iqbal","year":"2021","unstructured":"Iqbal D et al (2021) High-throughput screening and molecular dynamics simulation of natural product-like compounds against Alzheimer\u2019s disease through multitarget approach. Pharmaceuticals 14(9):937","journal-title":"Pharmaceuticals"},{"issue":"1","key":"1026_CR84","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1038\/nmeth.3658","volume":"13","author":"I Ivani","year":"2016","unstructured":"Ivani I et al (2016) Parmbsc1: a refined force field for DNA simulations. Nat Methods 13(1):55\u201358","journal-title":"Nat Methods"},{"issue":"49","key":"1026_CR85","doi-asserted-by":"publisher","first-page":"10347","DOI":"10.1021\/acs.jpcb.2c05151","volume":"126","author":"ME Izadi","year":"2022","unstructured":"Izadi ME, Sabzyan H (2022) Reactive molecular dynamics simulation of the structural damages of the B-DNA induced by the oxidation\/nitration of guanine. J Phys Chem B 126(49):10347\u201310359","journal-title":"J Phys Chem B"},{"issue":"4711","key":"1026_CR86","doi-asserted-by":"publisher","first-page":"422","DOI":"10.1038\/185422a0","volume":"185","author":"K JC","year":"1960","unstructured":"JC K et al (1960) Structure of myoglobin: A three-dimensional fourier synthesis at 2 A. resolution. Nature 185(4711):422\u2013427","journal-title":"Nature"},{"key":"1026_CR87","doi-asserted-by":"crossref","unstructured":"Jespers W, \u00c5qvist J (2021) and H. Guti\u00e9rrez-de-Ter\u00e1n, Free energy calculations for protein\u2013ligand binding prediction. Protein-Ligand Interactions and Drug Design, pp 203\u2013226","DOI":"10.1007\/978-1-0716-1209-5_12"},{"issue":"12","key":"1026_CR88","doi-asserted-by":"publisher","first-page":"3534","DOI":"10.1093\/jac\/dkaa376","volume":"75","author":"X Jiang","year":"2020","unstructured":"Jiang X et al (2020) Molecular dynamics simulations informed by membrane lipidomics reveal the structure\u2013interaction relationship of polymyxins with the lipid A-based outer membrane of Acinetobacter baumannii. J Antimicrob Chemother 75(12):3534\u20133543","journal-title":"J Antimicrob Chemother"},{"issue":"1","key":"1026_CR89","doi-asserted-by":"publisher","DOI":"10.1111\/1541-4337.13280","volume":"23","author":"Z Jin","year":"2024","unstructured":"Jin Z, Wei Z (2024) Molecular simulation for food protein\u2013ligand interactions: a comprehensive review on principles, current applications, and emerging trends. Compr Rev Food Sci Food Saf 23(1):e13280","journal-title":"Compr Rev Food Sci Food Saf"},{"issue":"7811","key":"1026_CR90","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1038\/s41586-020-2223-y","volume":"582","author":"Z Jin","year":"2020","unstructured":"Jin Z et al (2020) Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature 582(7811):289\u2013293","journal-title":"Nature"},{"issue":"9","key":"1026_CR91","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1038\/nsb0902-646","volume":"9","author":"M Karplus","year":"2002","unstructured":"Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat Struct Biol 9(9):646\u2013652","journal-title":"Nat Struct Biol"},{"issue":"1","key":"1026_CR92","doi-asserted-by":"publisher","first-page":"17716","DOI":"10.1038\/s41598-020-74468-0","volume":"10","author":"S Keretsu","year":"2020","unstructured":"Keretsu S, Bhujbal SP, Cho SJ (2020) Rational approach toward COVID-19 main protease inhibitors via molecular docking, molecular dynamics simulation and free energy calculation. Sci Rep 10(1):17716","journal-title":"Sci Rep"},{"issue":"41","key":"1026_CR93","doi-asserted-by":"publisher","first-page":"13958","DOI":"10.1039\/D1SC03472C","volume":"12","author":"Y Khalak","year":"2021","unstructured":"Khalak Y et al (2021) Alchemical absolute protein\u2013ligand binding free energies for drug design. Chem Sci 12(41):13958\u201313971","journal-title":"Chem Sci"},{"issue":"10","key":"1026_CR94","doi-asserted-by":"publisher","first-page":"3223","DOI":"10.1021\/ct1004438","volume":"6","author":"C Knight","year":"2010","unstructured":"Knight C et al (2010) Defining condensed phase reactive force fields from ab initio molecular dynamics simulations: the case of the hydrated excess proton. J Chem Theory Comput 6(10):3223\u20133232","journal-title":"J Chem Theory Comput"},{"issue":"11","key":"1026_CR95","doi-asserted-by":"publisher","first-page":"946","DOI":"10.1039\/D1ME00053E","volume":"6","author":"K Konstantinidis","year":"2021","unstructured":"Konstantinidis K et al (2021) On the estimation of the molecular inaccessible volume and the molecular accessible surface of a ligand in protein\u2013ligand systems. Mol Syst Des Eng 6(11):946\u2013963","journal-title":"Mol Syst Des Eng"},{"key":"1026_CR96","doi-asserted-by":"crossref","unstructured":"Kufareva I, Abagyan R (2012) Methods of protein structure comparison. Homology modeling: Methods and protocols, : pp. 231\u2013257","DOI":"10.1007\/978-1-61779-588-6_10"},{"key":"1026_CR97","doi-asserted-by":"publisher","DOI":"10.1016\/j.jep.2021.114647","volume":"284","author":"S Kumar","year":"2022","unstructured":"Kumar S, Singh B, Singh R (2022) Catharanthus roseus (L.) G. Don: a review of its ethnobotany, phytochemistry, ethnopharmacology and toxicities. J Ethnopharmacol 284:114647","journal-title":"J Ethnopharmacol"},{"issue":"11","key":"1026_CR98","doi-asserted-by":"publisher","first-page":"6717","DOI":"10.1007\/s11696-023-02971-5","volume":"77","author":"A Kumar","year":"2023","unstructured":"Kumar A (2023) Identification of potential DNA gyrase inhibitors: virtual screening, extra-precision docking and molecular dynamics simulation study. Chem Pap 77(11):6717\u20136727","journal-title":"Chem Pap"},{"issue":"3","key":"1026_CR99","doi-asserted-by":"publisher","first-page":"654","DOI":"10.1021\/acs.accounts.9b00613","volume":"53","author":"A Kuzmanic","year":"2020","unstructured":"Kuzmanic A et al (2020) Investigating cryptic binding sites by molecular dynamics simulations. Acc Chem Res 53(3):654\u2013661","journal-title":"Acc Chem Res"},{"key":"1026_CR100","doi-asserted-by":"publisher","first-page":"851","DOI":"10.1016\/j.enganabound.2022.11.018","volume":"146","author":"QH Le","year":"2023","unstructured":"Le QH (2023) A molecular dynamics investigation of the atomic structural behavior of the interaction between amyloid beta protein and aspirin within an aqueous nanodomain. Eng Anal Boundary Elem 146:851\u2013858","journal-title":"Eng Anal Boundary Elem"},{"issue":"5","key":"1026_CR101","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbac308","volume":"23","author":"C Lee","year":"2022","unstructured":"Lee C, Su B-H, Tseng YJ (2022) Comparative studies of AlphaFold, RosettaFold and Modeller: a case study involving the use of G-protein-coupled receptors. Brief Bioinform 23(5):bbac308","journal-title":"Brief Bioinform"},{"issue":"16","key":"1026_CR102","doi-asserted-by":"publisher","first-page":"2503","DOI":"10.1021\/acs.biochem.3c00165","volume":"62","author":"A Lester","year":"2023","unstructured":"Lester A et al (2023) Computational exploration of potential CFTR binding sites for type i corrector drugs. Biochemistry 62(16):2503\u20132515","journal-title":"Biochemistry"},{"issue":"29","key":"1026_CR103","doi-asserted-by":"publisher","DOI":"10.1002\/adfm.202315509","volume":"34","author":"L Li","year":"2024","unstructured":"Li L et al (2024a) Protein-based controllable nanoarchitectonics for desired applications. Adv Funct Mater 34(29):2315509","journal-title":"Adv Funct Mater"},{"issue":"2","key":"1026_CR104","doi-asserted-by":"publisher","DOI":"10.1002\/ppap.202300119","volume":"21","author":"Y Li","year":"2024","unstructured":"Li Y et al (2024b) Molecular dynamics simulation research on the interaction between plasma and living organisms: a comprehensive review. Plasma Process Polym 21(2):2300119","journal-title":"Plasma Process Polym"},{"issue":"4","key":"1026_CR105","doi-asserted-by":"publisher","first-page":"2014","DOI":"10.1021\/acs.jcim.4c01947","volume":"65","author":"C Li","year":"2025","unstructured":"Li C et al (2025) Comprehensive evaluation of End-Point free energy methods in DNA\u2013Ligand interaction predictions. J Chem Inf Model 65(4):2014\u20132025","journal-title":"J Chem Inf Model"},{"issue":"11","key":"1026_CR106","doi-asserted-by":"publisher","first-page":"7096","DOI":"10.1021\/acs.jctc.1c00682","volume":"17","author":"K Liebl","year":"2021","unstructured":"Liebl K, Zacharias M (2021) Tumuc1: a new accurate DNA force field consistent with high-level quantum chemistry. J Chem Theory Comput 17(11):7096\u20137105","journal-title":"J Chem Theory Comput"},{"issue":"4","key":"1026_CR107","first-page":"e1455","volume":"10","author":"V Limongelli","year":"2020","unstructured":"Limongelli V (2020) Ligand binding free energy and kinetics calculation in 2020. Wiley Interdisciplinary Reviews: Comput Mol Sci 10(4):e1455","journal-title":"Wiley Interdisciplinary Reviews: Comput Mol Sci"},{"key":"1026_CR108","doi-asserted-by":"publisher","first-page":"4481","DOI":"10.1016\/j.csbj.2022.08.034","volume":"20","author":"S Liu","year":"2022","unstructured":"Liu S, Wu K, Chen C (2022) Obtaining protein foldability information from computational models of AlphaFold2 and rosettafold. Comput Struct Biotechnol J 20:4481\u20134489","journal-title":"Comput Struct Biotechnol J"},{"key":"1026_CR109","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1134\/S0026893308040195","volume":"42","author":"MY Lobanov","year":"2008","unstructured":"Lobanov MY, Bogatyreva N, Galzitskaya O (2008) Radius of gyration as an indicator of protein structure compactness. Mol Biol 42:623\u2013628","journal-title":"Mol Biol"},{"issue":"2","key":"1026_CR110","doi-asserted-by":"publisher","first-page":"252","DOI":"10.3390\/polym14020252","volume":"14","author":"N Lukasheva","year":"2022","unstructured":"Lukasheva N et al (2022) Changes in the local conformational states caused by simple Na\u2009+\u2009and K\u2009+\u2009ions in polyelectrolyte simulations: comparison of seven force fields with and without NBFIX and ECC corrections. Polymers (Basel) 14(2):252","journal-title":"Polymers (Basel)"},{"issue":"11","key":"1026_CR111","doi-asserted-by":"publisher","first-page":"2965","DOI":"10.1016\/j.chempr.2021.05.021","volume":"7","author":"J Manigrasso","year":"2021","unstructured":"Manigrasso J, Marcia M, De Vivo M (2021) Computer-aided design of RNA-targeted small molecules: a growing need in drug discovery. Chem 7(11):2965\u20132988","journal-title":"Chem"},{"issue":"15","key":"1026_CR112","doi-asserted-by":"publisher","first-page":"4155","DOI":"10.1021\/j100066a040","volume":"98","author":"S-J Marrink","year":"1994","unstructured":"Marrink S-J, Berendsen HJ (1994) Simulation of water transport through a lipid membrane. J Phys Chem 98(15):4155\u20134168","journal-title":"J Phys Chem"},{"issue":"3","key":"1026_CR113","doi-asserted-by":"publisher","first-page":"e0119264","DOI":"10.1371\/journal.pone.0119264","volume":"10","author":"L Mart\u00ednez","year":"2015","unstructured":"Mart\u00ednez L (2015) Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis. PLoS ONE 10(3):e0119264","journal-title":"PLoS ONE"},{"issue":"5","key":"1026_CR114","doi-asserted-by":"publisher","first-page":"1529","DOI":"10.1021\/acs.jcim.2c01444","volume":"63","author":"Y Maruyama","year":"2023","unstructured":"Maruyama Y (2023) Analysis of protein folding simulation with moving root mean square deviation. J Chem Inf Model 63(5):1529\u20131541","journal-title":"J Chem Inf Model"},{"key":"1026_CR115","unstructured":"Matta DK (2021) Role of protonation state changes and hydrogen bonding around the oxygen evolving complex of photosystem II. City University of New York"},{"key":"1026_CR116","doi-asserted-by":"crossref","unstructured":"Mattick J, Amaral P (2023) RNA, the epicenter of genetic information. Taylor & Francis","DOI":"10.1201\/9781003109242"},{"issue":"5","key":"1026_CR117","doi-asserted-by":"publisher","first-page":"1030","DOI":"10.3390\/molecules25051030","volume":"25","author":"L Maveyraud","year":"2020","unstructured":"Maveyraud L, Mourey L (2020) Protein X-ray crystallography and drug discovery. Molecules 25(5):1030","journal-title":"Molecules"},{"issue":"2","key":"1026_CR118","doi-asserted-by":"publisher","first-page":"399","DOI":"10.17509\/ijost.v10i2.85146","volume":"10","author":"M Merzouki","year":"2025","unstructured":"Merzouki M et al (2025) Computational engineering of Malonate and tetrazole derivatives targeting SARS-CoV-2 main protease: pharmacokinetics, docking, and molecular dynamics insights to support the sustainable development goals (SDGs), with a bibliometric analysis. Indones J Sci Technol 10(2):399\u2013418","journal-title":"Indones J Sci Technol"},{"issue":"10","key":"1026_CR119","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1038\/s41580-019-0143-1","volume":"20","author":"EM Michalak","year":"2019","unstructured":"Michalak EM et al (2019) The roles of DNA, RNA and histone methylation in ageing and cancer. Nat Rev Mol Cell Biol 20(10):573\u2013589","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"21","key":"1026_CR120","doi-asserted-by":"publisher","first-page":"7241","DOI":"10.3390\/molecules27217241","volume":"27","author":"FJ Mirza","year":"2022","unstructured":"Mirza FJ et al (2022) Multitargeted molecular docking and dynamic simulation studies of bioactive compounds from Rosmarinus officinalis against alzheimer\u2019s disease. Molecules 27(21):7241","journal-title":"Molecules"},{"issue":"7","key":"1026_CR121","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1007\/s00706-023-03076-1","volume":"154","author":"M Mohanty","year":"2023","unstructured":"Mohanty M, Mohanty PS (2023) Molecular docking in organic, inorganic, and hybrid systems: a tutorial review. Monatshefte f\u00fcr Chemie-Chemical Monthly 154(7):683\u2013707","journal-title":"Monatshefte f\u00fcr Chemie-Chemical Monthly"},{"key":"1026_CR122","doi-asserted-by":"publisher","first-page":"e14120","DOI":"10.7717\/peerj.14120","volume":"10","author":"H Nada","year":"2022","unstructured":"Nada H, Elkamhawy A, Lee K (2022) Identification of 1H-purine-2, 6-dione derivative as a potential SARS-CoV-2 main protease inhibitor: molecular docking, dynamic simulations, and energy calculations. PeerJ 10:e14120","journal-title":"PeerJ"},{"issue":"11","key":"1026_CR123","doi-asserted-by":"publisher","first-page":"3264","DOI":"10.3390\/molecules26113264","volume":"26","author":"AS Nair","year":"2021","unstructured":"Nair AS et al (2021) Development of halogenated pyrazolines as selective monoamine oxidase-B inhibitors: deciphering via molecular dynamics approach. Molecules 26(11):3264","journal-title":"Molecules"},{"key":"1026_CR124","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiomed.2022.106407","volume":"152","author":"A Narayan","year":"2023","unstructured":"Narayan A et al (2023) UncertainSCI: uncertainty quantification for computational models in biomedicine and bioengineering. Comput Biol Med 152:106407","journal-title":"Comput Biol Med"},{"issue":"1","key":"1026_CR125","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1080\/14756366.2022.2134997","volume":"38","author":"GSd Oliveira","year":"2023","unstructured":"Oliveira GSd et al (2023) Prospecting in silico antibacterial activity of a peptide from trypsin inhibitor isolated from tamarind seed. J Enzyme Inhib Med Chem 38(1):67\u201383","journal-title":"J Enzyme Inhib Med Chem"},{"issue":"1","key":"1026_CR126","doi-asserted-by":"publisher","first-page":"6296","DOI":"10.1038\/s41598-024-56893-7","volume":"14","author":"L Pallante","year":"2024","unstructured":"Pallante L et al (2024) Virtuouspocketome: a computational tool for screening protein\u2013ligand complexes to identify similar binding sites. Sci Rep 14(1):6296","journal-title":"Sci Rep"},{"key":"1026_CR127","doi-asserted-by":"crossref","unstructured":"Panchalingam S, Kasivelu G, Jayaraman M (2025) Computational modeling and molecular dynamic simulations of gold nanoparticles, in Gold Nanoparticles, nanomaterials and nanocomposites. Elsevier, pp 869\u2013893","DOI":"10.1016\/B978-0-443-15897-1.00022-4"},{"key":"1026_CR128","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1016\/j.csbj.2019.12.004","volume":"18","author":"T Pantsar","year":"2020","unstructured":"Pantsar T (2020) The current understanding of KRAS protein structure and dynamics. Comput Struct Biotechnol J 18:189\u2013198","journal-title":"Comput Struct Biotechnol J"},{"issue":"12","key":"1026_CR129","doi-asserted-by":"publisher","first-page":"e66","DOI":"10.1038\/emm.2013.97","volume":"45","author":"BS Park","year":"2013","unstructured":"Park BS, Lee J-O (2013) Recognition of lipopolysaccharide pattern by TLR4 complexes. Exp Mol Med 45(12):e66\u2013e66","journal-title":"Exp Mol Med"},{"key":"1026_CR130","doi-asserted-by":"publisher","DOI":"10.1016\/j.antiviral.2023.105740","volume":"220","author":"PP Parvatikar","year":"2023","unstructured":"Parvatikar PP et al (2023) Artificial intelligence: machine learning approach for screening large database and drug discovery. Antiviral Res 220:105740","journal-title":"Antiviral Res"},{"issue":"4","key":"1026_CR131","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1016\/S0959-440X(94)90209-7","volume":"4","author":"RW Pastor","year":"1994","unstructured":"Pastor RW (1994) Molecular dynamics and monte carlo simulations of lipid bilayers. Curr Opin Struct Biol 4(4):486\u2013492","journal-title":"Curr Opin Struct Biol"},{"key":"1026_CR132","doi-asserted-by":"publisher","first-page":"539","DOI":"10.2165\/11591860-000000000-00000","volume":"28","author":"L Patel","year":"2011","unstructured":"Patel L, Grossberg GT (2011) Combination therapy for Alzheimer\u2019s disease. Drugs Aging 28:539\u2013546","journal-title":"Drugs Aging"},{"issue":"4","key":"1026_CR133","doi-asserted-by":"publisher","first-page":"1491","DOI":"10.1080\/07391102.2020.1734092","volume":"39","author":"HM Patel","year":"2021","unstructured":"Patel HM et al (2021a) In Silico search of triple mutant T790M\/C797S allosteric inhibitors to conquer acquired resistance problem in non-small cell lung cancer (NSCLC): a combined approach of structure-based virtual screening and molecular dynamics simulation. J Biomol Struct Dyn 39(4):1491\u20131505","journal-title":"J Biomol Struct Dyn"},{"issue":"8","key":"1026_CR134","doi-asserted-by":"publisher","first-page":"2838","DOI":"10.1080\/07391102.2020.1754918","volume":"39","author":"HM Patel","year":"2021","unstructured":"Patel HM et al (2021b) BREED based de novo hybridization approach: generating novel T790M\/C797S-EGFR tyrosine kinase inhibitors to overcome the problem of mutation and resistance in Non small cell lung cancer (NSCLC). J Biomol Struct Dyn 39(8):2838\u20132856","journal-title":"J Biomol Struct Dyn"},{"key":"1026_CR135","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejmcr.2024.100133","volume":"10","author":"VM Patil","year":"2024","unstructured":"Patil VM et al (2024) Experimental and computational models to understand protein-ligand, metal-ligand and metal-DNA interactions pertinent to targeted cancer and other therapies. European Journal of Medicinal Chemistry Reports 10:100133","journal-title":"European Journal of Medicinal Chemistry Reports"},{"issue":"2","key":"1026_CR136","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1080\/17476348.2019.1562339","volume":"13","author":"P Peyrani","year":"2019","unstructured":"Peyrani P et al (2019) The burden of community-acquired bacterial pneumonia in the era of antibiotic resistance. Expert Rev Respir Med 13(2):139\u2013152","journal-title":"Expert Rev Respir Med"},{"issue":"4","key":"1026_CR137","doi-asserted-by":"publisher","first-page":"2494","DOI":"10.1021\/acs.jctc.9b00251","volume":"16","author":"S Piana","year":"2020","unstructured":"Piana S et al (2020) Development of a force field for the simulation of single-chain proteins and protein\u2013protein complexes. J Chem Theory Comput 16(4):2494\u20132507","journal-title":"J Chem Theory Comput"},{"issue":"14","key":"1026_CR138","doi-asserted-by":"publisher","first-page":"3302","DOI":"10.1021\/acs.jpcb.3c07335","volume":"128","author":"A Pirnia","year":"2024","unstructured":"Pirnia A (2024) Perspective on integrative simulations of bioenergetic domains. J Phys Chem B 128(14):3302\u20133319","journal-title":"J Phys Chem B"},{"key":"1026_CR139","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejmech.2020.112764","volume":"207","author":"Y Qiu","year":"2020","unstructured":"Qiu Y et al (2020) Computational methods-guided design of modulators targeting protein-protein interactions (PPIs). Eur J Med Chem 207:112764","journal-title":"Eur J Med Chem"},{"issue":"1","key":"1026_CR140","doi-asserted-by":"publisher","first-page":"213","DOI":"10.4161\/viru.27024","volume":"5","author":"G Ramachandran","year":"2014","unstructured":"Ramachandran G (2014) Gram-positive and gram-negative bacterial toxins in sepsis: a brief review. Virulence 5(1):213\u2013218","journal-title":"Virulence"},{"issue":"7","key":"1026_CR141","doi-asserted-by":"publisher","first-page":"471","DOI":"10.2217\/fvl-2020-0137","volume":"15","author":"M Rehman","year":"2020","unstructured":"Rehman M et al (2020) Therapeutic and vaccine strategies against SARS-CoV-2: past, present and future. Future Virol 15(7):471\u2013482","journal-title":"Future Virol"},{"issue":"3","key":"1026_CR142","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1080\/17460441.2023.2171396","volume":"18","author":"AU Rehman","year":"2023","unstructured":"Rehman AU et al (2023) Computational approaches for the design of modulators targeting protein-protein interactions. Expert Opin Drug Discov 18(3):315\u2013333","journal-title":"Expert Opin Drug Discov"},{"key":"1026_CR143","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2020.00114","volume":"7","author":"EA Rifai","year":"2020","unstructured":"Rifai EA, Van Dijk M, Geerke DP (2020) Recent developments in linear interaction energy based binding free energy calculations. Front Mol Biosci 7:114","journal-title":"Front Mol Biosci"},{"key":"1026_CR144","doi-asserted-by":"publisher","DOI":"10.1016\/j.antiviral.2022.105270","volume":"200","author":"M Sachse","year":"2022","unstructured":"Sachse M et al (2022) Unraveling the antiviral activity of plitidepsin against SARS-CoV-2 by subcellular and morphological analysis. Antiviral Res 200:105270","journal-title":"Antiviral Res"},{"issue":"1","key":"1026_CR145","doi-asserted-by":"publisher","first-page":"6849","DOI":"10.1038\/s41598-021-86211-4","volume":"11","author":"AS Sadr","year":"2021","unstructured":"Sadr AS et al (2021) In silico studies reveal structural deviations of mutant profilin-1 and interaction with riluzole and edaravone in amyotrophic lateral sclerosis. Sci Rep 11(1):6849","journal-title":"Sci Rep"},{"issue":"1","key":"1026_CR146","doi-asserted-by":"publisher","DOI":"10.3390\/pr9010071","volume":"9","author":"OM Salo-Ahen","year":"2020","unstructured":"Salo-Ahen OM (2020) Molecular dynamics simulations in drug discovery and pharmaceutical development. Processes 9(1):71","journal-title":"Processes"},{"issue":"8","key":"1026_CR147","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1038\/s41576-018-0013-2","volume":"19","author":"M Schmid","year":"2018","unstructured":"Schmid M, Jensen TH (2018) Controlling nuclear RNA levels. Nat Rev Genet 19(8):518\u2013529","journal-title":"Nat Rev Genet"},{"key":"1026_CR148","doi-asserted-by":"crossref","unstructured":"Shastry KA, Sanjay H (2021) Computational intelligence, machine learning and deep learning techniques for effective future predictions of COVID-19: a review. Understanding COVID-19: The Role of Computational Intelligence, : pp. 379\u2013402","DOI":"10.1007\/978-3-030-74761-9_17"},{"key":"1026_CR149","doi-asserted-by":"crossref","unstructured":"Shukla R, Tripathi T (2020) Molecular dynamics simulation of protein and protein\u2013ligand complexes. Computer-aided drug design, : pp. 133\u2013161","DOI":"10.1007\/978-981-15-6815-2_7"},{"key":"1026_CR150","doi-asserted-by":"crossref","unstructured":"Singh S, Baker QB, Singh DB (2022a) Molecular Docking and molecular dynamics simulation, in Bioinformatics. Elsevier, pp 291\u2013304","DOI":"10.1016\/B978-0-323-89775-4.00014-6"},{"issue":"10","key":"1026_CR151","doi-asserted-by":"publisher","first-page":"4069","DOI":"10.1039\/D2MA00067A","volume":"3","author":"V Singh","year":"2022","unstructured":"Singh V (2022) Recent trends in computational tools and data-driven modeling for advanced materials. Mater Adv 3(10):4069\u20134087","journal-title":"Mater Adv"},{"issue":"10","key":"1026_CR152","doi-asserted-by":"publisher","first-page":"3649","DOI":"10.1080\/07391102.2020.1768149","volume":"39","author":"MF Sk","year":"2021","unstructured":"Sk MF et al (2021) Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations. J Biomol Struct Dyn 39(10):3649\u20133661","journal-title":"J Biomol Struct Dyn"},{"key":"1026_CR153","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiomed.2020.104054","volume":"126","author":"S Skariyachan","year":"2020","unstructured":"Skariyachan S et al (2020) Structural and molecular basis of the interaction mechanism of selected drugs towards multiple targets of SARS-CoV-2 by molecular docking and dynamic simulation studies-deciphering the scope of repurposed drugs. Comput Biol Med 126:104054","journal-title":"Comput Biol Med"},{"key":"1026_CR154","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1016\/bs.apcsb.2015.09.004","volume":"102","author":"P Sneha","year":"2016","unstructured":"Sneha P, Doss CGP (2016) Molecular dynamics: new frontier in personalized medicine. Adv Protein Chem Struct Biol 102:181\u2013224","journal-title":"Adv Protein Chem Struct Biol"},{"issue":"1","key":"1026_CR155","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1080\/17512433.2017.1265446","volume":"10","author":"K Soejima","year":"2017","unstructured":"Soejima K, Yasuda H, Hirano T (2017) Osimertinib for EGFR T790M mutation-positive non-small cell lung cancer. Expert Rev Clin Pharmacol 10(1):31\u201338","journal-title":"Expert Rev Clin Pharmacol"},{"issue":"11","key":"1026_CR156","doi-asserted-by":"publisher","first-page":"1729","DOI":"10.3390\/life12111729","volume":"12","author":"SS Sohrab","year":"2022","unstructured":"Sohrab SS, Kamal MA (2022) Screening, docking, and molecular dynamics study of natural compounds as an anti-HER2 for the management of breast cancer. Life 12(11):1729","journal-title":"Life"},{"issue":"1","key":"1026_CR157","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-26689-7","volume":"8","author":"V Solanki","year":"2018","unstructured":"Solanki V, Tiwari V (2018a) Subtractive proteomics to identify novel drug targets and reverse vaccinology for the development of chimeric vaccine against Acinetobacter baumannii. Sci Rep 8(1):9044","journal-title":"Sci Rep"},{"issue":"1","key":"1026_CR158","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-018-26689-7","volume":"8","author":"V Solanki","year":"2018","unstructured":"Solanki V, Tiwari V (2018b) Subtractive proteomics to identify novel drug targets and reverse vaccinology for the development of chimeric vaccine against Acinetobacter baumannii. Sci Rep 8(1):1\u201319","journal-title":"Sci Rep"},{"issue":"6328","key":"1026_CR159","doi-asserted-by":"publisher","first-page":"966","DOI":"10.1126\/science.aai8636","volume":"355","author":"V Spahn","year":"2017","unstructured":"Spahn V et al (2017) A nontoxic pain killer designed by modeling of pathological receptor conformations. Science 355(6328):966\u2013969","journal-title":"Science"},{"issue":"8","key":"1026_CR160","doi-asserted-by":"publisher","DOI":"10.1021\/acs.chemrev.7b00427","volume":"118","author":"J \u0160poner","year":"2018","unstructured":"\u0160poner J et al (2018) RNA structural dynamics as captured by molecular simulations: a comprehensive overview. Chem Rev 118(8):4177","journal-title":"Chem Rev"},{"issue":"5","key":"1026_CR161","doi-asserted-by":"publisher","first-page":"e36312","DOI":"10.1371\/journal.pone.0036312","volume":"7","author":"AJ Standish","year":"2012","unstructured":"Standish AJ et al (2012) Chemical inhibition of bacterial protein tyrosine phosphatase suppresses capsule production. PLoS ONE 7(5):e36312","journal-title":"PLoS ONE"},{"issue":"11","key":"1026_CR162","doi-asserted-by":"publisher","first-page":"7861","DOI":"10.3390\/molecules15117861","volume":"15","author":"SCW Sze","year":"2010","unstructured":"Sze SCW et al (2010) Herba epimedii: anti-oxidative properties and its medical implications. Molecules 15(11):7861\u20137870","journal-title":"Molecules"},{"key":"1026_CR163","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.crstbi.2020.11.002","volume":"3","author":"KP Tan","year":"2021","unstructured":"Tan KP et al (2021) Peptide bond planarity constrains hydrogen bond geometry and influences secondary structure conformations. Curr Res Struct Biol 3:1\u20138","journal-title":"Curr Res Struct Biol"},{"issue":"10","key":"1026_CR164","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msac197","volume":"39","author":"Q-Y Tang","year":"2022","unstructured":"Tang Q-Y (2022) The statistical trends of protein evolution: a lesson from alphafold database. Mol Biol Evol 39(10):msac197","journal-title":"Mol Biol Evol"},{"issue":"4","key":"1026_CR165","doi-asserted-by":"publisher","first-page":"e00109","DOI":"10.1128\/CMR.00109-21","volume":"34","author":"K Tao","year":"2021","unstructured":"Tao K et al (2021) SARS-CoV-2 antiviral therapy. Clin Microbiol Rev 34(4):e00109\u2013e00121","journal-title":"Clin Microbiol Rev"},{"issue":"11","key":"1026_CR166","doi-asserted-by":"publisher","first-page":"833","DOI":"10.1038\/nrm2039","volume":"7","author":"NK Tonks","year":"2006","unstructured":"Tonks NK (2006) Protein tyrosine phosphatases: from genes, to function, to disease. Nat Rev Mol Cell Biol 7(11):833\u2013846","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"4","key":"1026_CR167","doi-asserted-by":"publisher","first-page":"78","DOI":"10.3390\/computation12040078","volume":"12","author":"N Tshilande","year":"2024","unstructured":"Tshilande N, Mammino L, Bilonda MK (2024) The study of molecules and processes in solution: an overview of questions, approaches and applications. Computation 12(4):78","journal-title":"Computation"},{"issue":"11","key":"1026_CR168","doi-asserted-by":"publisher","first-page":"1233","DOI":"10.1080\/17460441.2021.1942836","volume":"16","author":"T Tuccinardi","year":"2021","unstructured":"Tuccinardi T (2021) What is the current value of MM\/PBSA and MM\/GBSA methods in drug discovery? Expert Opin Drug Discov 16(11):1233\u20131237","journal-title":"Expert Opin Drug Discov"},{"issue":"24","key":"1026_CR169","doi-asserted-by":"publisher","first-page":"4442","DOI":"10.1021\/acs.jpcb.1c10971","volume":"126","author":"MR Tucker","year":"2022","unstructured":"Tucker MR et al (2022) Development of force field parameters for the simulation of single-and double-stranded DNA molecules and DNA\u2013protein complexes. J Phys Chem B 126(24):4442\u20134457","journal-title":"J Phys Chem B"},{"key":"1026_CR170","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijpharm.2023.122739","volume":"635","author":"C Vairo","year":"2023","unstructured":"Vairo C et al (2023a) Colistin-and amikacin-loaded lipid-based drug delivery systems for resistant gram-negative lung and wound bacterial infections. Int J Pharm 635:122739","journal-title":"Int J Pharm"},{"key":"1026_CR171","doi-asserted-by":"crossref","unstructured":"Vairo C et al (2023b) Colistin-and Amikacin-loaded lipid-based drug delivery systems for resistant gram-negative lung and wound bacterial infections. Int J Pharm, : p. 122739","DOI":"10.1016\/j.ijpharm.2023.122739"},{"key":"1026_CR172","doi-asserted-by":"crossref","unstructured":"Varona JF et al (2022) Preclinical and randomized phase I studies of plitidepsin in adults hospitalized with COVID-19. Life science alliance, 5(4)","DOI":"10.26508\/lsa.202101200"},{"key":"1026_CR173","unstructured":"Venkatakrishnan A (2017) GPCR dynamics: structures in motion."},{"issue":"5","key":"1026_CR174","doi-asserted-by":"publisher","first-page":"1182","DOI":"10.1080\/07391102.2017.1317025","volume":"36","author":"P Verma","year":"2018","unstructured":"Verma P, Tiwari M, Tiwari V (2018) Silico high-throughput virtual screening and molecular dynamics simulation study to identify inhibitor for AdeABC efflux pump of acinetobacter baumannii. J Biomol Struct Dyn 36(5):1182\u20131194","journal-title":"J Biomol Struct Dyn"},{"key":"1026_CR175","doi-asserted-by":"crossref","unstructured":"Vishvakarma VK et al (2022a) Hunting the main protease of SARS-CoV-2 by plitidepsin: Molecular docking and temperature-dependent molecular dynamics simulations. Amino acids, : pp. 1\u20139","DOI":"10.1007\/s00726-021-03098-1"},{"issue":"2","key":"1026_CR176","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1007\/s00726-021-03098-1","volume":"54","author":"VK Vishvakarma","year":"2022","unstructured":"Vishvakarma VK et al (2022b) Hunting the main protease of SARS-CoV-2 by plitidepsin: molecular docking and temperature-dependent molecular dynamics simulations. Amino Acids 54(2):205\u2013213","journal-title":"Amino Acids"},{"key":"1026_CR177","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpc.2021.106541","volume":"271","author":"J Wan","year":"2021","unstructured":"Wan J et al (2021) Molecular dynamics simulations reveal the destabilization mechanism of Alzheimer\u2019s disease-related Tau R3-R4 protofilament by norepinephrine. Biophys Chem 271:106541","journal-title":"Biophys Chem"},{"issue":"1","key":"1026_CR178","doi-asserted-by":"publisher","DOI":"10.1155\/2022\/3720026","volume":"2022","author":"Z Wang","year":"2022","unstructured":"Wang Z et al (2022a) Exploring the resistance mechanisms of distal D835V mutation in FLT3 to inhibitors. Oxid Med Cell Longev 2022(1):3720026","journal-title":"Oxid Med Cell Longev"},{"issue":"1","key":"1026_CR179","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1186\/s12906-022-03732-9","volume":"22","author":"X Wang","year":"2022","unstructured":"Wang X et al (2022b) Pharmacological mechanism and therapeutic efficacy of Icariside II in the treatment of acute ischemic stroke: a systematic review and network pharmacological analysis. BMC Complement Med Ther 22(1):253","journal-title":"BMC Complement Med Ther"},{"issue":"1","key":"1026_CR180","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12906-022-03732-9","volume":"22","author":"X Wang","year":"2022","unstructured":"Wang X et al (2022c) Pharmacological mechanism and therapeutic efficacy of Icariside II in the treatment of acute ischemic stroke: a systematic review and network pharmacological analysis. BMC Complement Med Ther 22(1):1\u201318","journal-title":"BMC Complement Med Ther"},{"issue":"3","key":"1026_CR181","doi-asserted-by":"publisher","first-page":"371a","DOI":"10.1016\/j.bpj.2022.11.2043","volume":"122","author":"D Weerakoon","year":"2023","unstructured":"Weerakoon D et al (2023) Interactions of polymyxin B1 with the gram-negative inner membrane: A simulation study. Biophys J 122(3):371a","journal-title":"Biophys J"},{"issue":"1","key":"1026_CR182","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbab540","volume":"23","author":"J Wei","year":"2022","unstructured":"Wei J et al (2022) Protein\u2013RNA interaction prediction with deep learning: structure matters. Brief Bioinform 23(1):bbab540","journal-title":"Brief Bioinform"},{"issue":"10","key":"1026_CR183","doi-asserted-by":"publisher","first-page":"2902","DOI":"10.1021\/acs.jcim.3c00151","volume":"63","author":"S Wolf","year":"2023","unstructured":"Wolf S (2023) Predicting protein\u2013ligand binding and unbinding kinetics with biased MD simulations and coarse-graining of dynamics: current state and challenges. J Chem Inf Model 63(10):2902\u20132910","journal-title":"J Chem Inf Model"},{"issue":"2","key":"1026_CR184","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1517\/13543784.2014.848853","volume":"23","author":"Z-Q Xu","year":"2014","unstructured":"Xu Z-Q, Flavin MT, Flavin J (2014) Combating multidrug-resistant gram-negative bacterial infections. Expert Opin Investig Drugs 23(2):163\u2013182","journal-title":"Expert Opin Investig Drugs"},{"key":"1026_CR185","doi-asserted-by":"publisher","first-page":"692200","DOI":"10.3389\/fchem.2021.692200","volume":"9","author":"M Xu","year":"2021","unstructured":"Xu M, Zhu T, Zhang JZ (2021) Automatically constructed neural network potentials for molecular dynamics simulation of zinc proteins. Front Chem 9:692200","journal-title":"Front Chem"},{"key":"1026_CR186","doi-asserted-by":"crossref","unstructured":"Yang S, Kar S, Leszczynski J (2023) Tools and software for computer-aided drug design and discovery. Cheminformatics, QSAR and machine learning applications for novel drug development. Elsevier, pp 637\u2013661","DOI":"10.1016\/B978-0-443-18638-7.00017-7"},{"key":"1026_CR187","doi-asserted-by":"publisher","first-page":"4849","DOI":"10.1016\/j.csbj.2023.09.024","volume":"21","author":"AA Yekeen","year":"2023","unstructured":"Yekeen AA et al (2023) CHAPERONg: A tool for automated GROMACS-based molecular dynamics simulations and trajectory analyses. Comput Struct Biotechnol J 21:4849\u20134858","journal-title":"Comput Struct Biotechnol J"},{"issue":"1","key":"1026_CR188","doi-asserted-by":"publisher","first-page":"430","DOI":"10.1021\/acs.jctc.5b00967","volume":"12","author":"J Yoo","year":"2016","unstructured":"Yoo J, Aksimentiev A (2016) Improved parameterization of amine\u2013carboxylate and amine\u2013phosphate interactions for molecular dynamics simulations using the CHARMM and AMBER force fields. J Chem Theory Comput 12(1):430\u2013443","journal-title":"J Chem Theory Comput"},{"key":"1026_CR189","doi-asserted-by":"publisher","DOI":"10.1016\/j.lfs.2020.118621","volume":"264","author":"Z Zaman","year":"2021","unstructured":"Zaman Z (2021) Targeting protein tyrosine phosphatase to unravel possible inhibitors for Streptococcus pneumoniae using molecular docking, molecular dynamics simulations coupled with free energy calculations. Life Sci 264:118621","journal-title":"Life Sci"},{"issue":"7","key":"1026_CR190","doi-asserted-by":"publisher","first-page":"3154","DOI":"10.1021\/acs.jcim.4c02441","volume":"65","author":"J Zeng","year":"2025","unstructured":"Zeng J et al (2025) DeePMD-GNN: a DeePMD-kit plugin for external graph neural network potentials. J Chem Inf Model 65(7):3154\u20133160","journal-title":"J Chem Inf Model"},{"issue":"6489","key":"1026_CR191","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1126\/science.abb3405","volume":"368","author":"L Zhang","year":"2020","unstructured":"Zhang L et al (2020) Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved \u03b1-ketoamide inhibitors. Science 368(6489):409\u2013412","journal-title":"Science"},{"key":"1026_CR192","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1016\/j.biopha.2018.10.201","volume":"111","author":"J Zhou","year":"2019","unstructured":"Zhou J et al (2019) Icariside II attenuates lipopolysaccharide-induced neuroinflammation through inhibiting TLR4\/MyD88\/NF-\u03baB pathway in rats. Biomed Pharmacother 111:315\u2013324","journal-title":"Biomed Pharmacother"},{"issue":"1","key":"1026_CR193","volume":"10","author":"K-F Zhu","year":"2023","unstructured":"Zhu K-F (2023) Applications and prospects of cryo-EM in drug discovery. Mil Med Res 10(1):10","journal-title":"Mil Med Res"}],"container-title":["Biological Cybernetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00422-025-01026-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00422-025-01026-0\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00422-025-01026-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,10]],"date-time":"2025-12-10T08:02:29Z","timestamp":1765353749000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00422-025-01026-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,26]]},"references-count":193,"journal-issue":{"issue":"4-6","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["1026"],"URL":"https:\/\/doi.org\/10.1007\/s00422-025-01026-0","relation":{},"ISSN":["1432-0770"],"issn-type":[{"value":"1432-0770","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,26]]},"assertion":[{"value":"20 July 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 September 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 September 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"28"}}