{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,12]],"date-time":"2025-07-12T01:02:28Z","timestamp":1752282148450,"version":"3.32.0"},"reference-count":95,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T00:00:00Z","timestamp":1685577600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T00:00:00Z","timestamp":1685577600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T00:00:00Z","timestamp":1685577600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T00:00:00Z","timestamp":1685577600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T00:00:00Z","timestamp":1685577600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T00:00:00Z","timestamp":1685577600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T00:00:00Z","timestamp":1685577600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"content-domain":{"domain":["clinicalkey.fr","clinicalkey.jp","clinicalkey.com.au","clinicalkey.es","clinicalkey.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Computers in Biology and Medicine"],"published-print":{"date-parts":[[2023,6]]},"DOI":"10.1016\/j.compbiomed.2023.106965","type":"journal-article","created":{"date-parts":[[2023,4,20]],"date-time":"2023-04-20T20:38:23Z","timestamp":1682023103000},"page":"106965","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":5,"special_numbering":"C","title":["Structure based virtual screening, molecular dynamic simulation to identify the oxadiazole derivatives as inhibitors of Enterococcus D-Ala-D-Ser ligase for combating vancomycin resistance"],"prefix":"10.1016","volume":"159","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3688-0850","authenticated-orcid":false,"given":"Sneha B.","family":"Paymal","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5820-2412","authenticated-orcid":false,"given":"Sagar S.","family":"Barale","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shirishkumar V.","family":"Supanekar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0156-7466","authenticated-orcid":false,"given":"Kailas D.","family":"Sonawane","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"year":"2018","series-title":"WHO Report on Surveillance of Antibiotic Consumption: 2016-2018 Early Implementation","key":"10.1016\/j.compbiomed.2023.106965_bib1"},{"key":"10.1016\/j.compbiomed.2023.106965_bib2","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1016\/j.arcmed.2005.06.009","article-title":"Resistance to antibiotics: are we in the post-antibiotic era?","volume":"36","author":"Alanis","year":"2005","journal-title":"Arch. Med. Res."},{"key":"10.1016\/j.compbiomed.2023.106965_bib3","doi-asserted-by":"crossref","first-page":"9444","DOI":"10.1002\/jcb.27261","article-title":"Insights into the antibiotic resistance and inhibition mechanism of aminoglycoside phosphotransferase from Bacillus cereus: in silico and in vitro perspective","volume":"119","author":"Parulekar","year":"2018","journal-title":"J. Cell. Biochem."},{"key":"10.1016\/j.compbiomed.2023.106965_bib4","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1007\/s42770-019-00132-z","article-title":"Antibiotic resistance and inhibition mechanism of novel aminoglycoside phosphotransferase APH(5) from B. subtilis subsp. subtilis strain RK","volume":"50","author":"Parulekar","year":"2019","journal-title":"Braz. J. Microbiol."},{"key":"10.1016\/j.compbiomed.2023.106965_bib5","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.jep.2018.04.031","article-title":"Biofilm inhibition mechanism from extract of Hymenocallis littoralis leaves","volume":"222","author":"Nadaf","year":"2018","journal-title":"J. Ethnopharmacol."},{"year":"2019","series-title":"Antibiotic Resistance Threats in the United States, 2019","key":"10.1016\/j.compbiomed.2023.106965_bib6"},{"key":"10.1016\/j.compbiomed.2023.106965_bib7","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1007\/BF01963632","article-title":"Movable genetic elements and antibiotic resistance in enterococci","volume":"9","author":"B Clewell","year":"1990","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"10.1016\/j.compbiomed.2023.106965_bib8","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1038\/nrmicro2761","article-title":"The rise of the Enterococcus: beyond vancomycin resistance","volume":"10","author":"Arias","year":"2012","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.compbiomed.2023.106965_bib9","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1128\/CMR.13.4.686","article-title":"Vancomycin-resistant enterococci","volume":"13","author":"Cetinkaya","year":"2000","journal-title":"Clin. Microbiol. Rev."},{"key":"10.1016\/j.compbiomed.2023.106965_bib10","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/0966-842X(96)10063-9","article-title":"Glycopeptide resistance in enterococci","volume":"4","author":"Arthur","year":"1996","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.compbiomed.2023.106965_bib11","doi-asserted-by":"crossref","first-page":"468","DOI":"10.1021\/ar00022a006","article-title":"D-Alanyl-D-alanine ligases and the molecular mechanism of vancomycin resistance","volume":"25","author":"Wright","year":"1992","journal-title":"Acc. Chem. Res."},{"key":"10.1016\/j.compbiomed.2023.106965_bib12","doi-asserted-by":"crossref","first-page":"1021","DOI":"10.1042\/bj3041021","article-title":"Association constants for the binding of vancomycin and teicoplanin to N-acetyl-D-alanyl-D-alanine and N-acetyl-D-alanyl-D-serine","volume":"304","author":"Billot-Klein","year":"1994","journal-title":"Biochem. J."},{"key":"10.1016\/j.compbiomed.2023.106965_bib13","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1016\/S1074-5521(98)90633-0","article-title":"Active-site mutants of the VanC2 D-alanyl-D-serine ligase, characteristic of one vancomycin-resistant bacterial phenotype, revert towards wild-type D-alanyl-D-alanine ligases","volume":"5","author":"Healy","year":"1998","journal-title":"Chem. Biol."},{"key":"10.1016\/j.compbiomed.2023.106965_bib14","doi-asserted-by":"crossref","first-page":"4714","DOI":"10.1021\/jm990361t","article-title":"Vancomycin binding to low-affinity ligands: delineating a minimum set of interactions necessary for high-affinity binding","volume":"42","author":"Loll","year":"1999","journal-title":"J. Med. Chem."},{"issue":"Suppl 1","key":"10.1016\/j.compbiomed.2023.106965_bib15","doi-asserted-by":"crossref","first-page":"S25","DOI":"10.1086\/491711","article-title":"Vancomycin resistance in gram-positive cocci","volume":"42","author":"Courvalin","year":"2006","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.compbiomed.2023.106965_bib16","doi-asserted-by":"crossref","first-page":"4643","DOI":"10.1128\/AAC.01710-09","article-title":"vanM, a new glycopeptide resistance gene cluster found in Enterococcus faecium","volume":"54","author":"Xu","year":"2010","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.compbiomed.2023.106965_bib17","doi-asserted-by":"crossref","first-page":"2667","DOI":"10.1128\/AAC.01516-07","article-title":"Molecular characterization of Enterococcus faecalis N06-0364 with low-level vancomycin resistance harboring a novel D-Ala-D-Ser gene cluster, vanL","volume":"52","author":"Boyd","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.compbiomed.2023.106965_bib18","doi-asserted-by":"crossref","first-page":"4606","DOI":"10.1128\/AAC.00714-11","article-title":"D-Ala-d-Ser VanN-type transferable vancomycin resistance in Enterococcus faecium","volume":"55","author":"Lebreton","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.compbiomed.2023.106965_bib19","doi-asserted-by":"crossref","first-page":"2161","DOI":"10.1128\/AAC.43.9.2161","article-title":"VanE, a new type of acquired glycopeptide resistance in Enterococcus faecalis BM4405","volume":"43","author":"Fines","year":"1999","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.compbiomed.2023.106965_bib20","doi-asserted-by":"crossref","first-page":"37583","DOI":"10.1074\/jbc.M112.405522","article-title":"Structural and functional characterization of VanG D-Ala: D-Ser ligase associated with vancomycin resistance in Enterococcus faecalis","volume":"287","author":"Meziane-Cherif","year":"2012","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.compbiomed.2023.106965_bib21","first-page":"5","article-title":"Analysis of peptidoglycan precursors in vancomycin-resistant Enterococcus gallinarum BM4174 Biochem","volume":"301","author":"Reynolds","year":"1994","journal-title":"J"},{"issue":"D1","key":"10.1016\/j.compbiomed.2023.106965_bib22","doi-asserted-by":"crossref","first-page":"D1121","DOI":"10.1093\/nar\/gkx1076","article-title":"Therapeutic target database update 2018: enriched resource for facilitating bench-to-clinic research of targeted therapeutics","volume":"46","author":"Li","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiomed.2023.106965_bib23","doi-asserted-by":"crossref","first-page":"2566","DOI":"10.2174\/092986709788682029","article-title":"DD-ligases as a potential target for antibiotics: past, present, and future","volume":"16","author":"Tytgat","year":"2009","journal-title":"Curr. Med. Chem."},{"key":"10.1016\/j.compbiomed.2023.106965_bib24","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1093\/jac\/47.2.203","article-title":"Synergic activity of D-cycloserine and beta-chloro-D-alanine against","volume":"47","author":"David","year":"2001","journal-title":"Mycobacterium tuberculosis. J. Antimicrob. Chemother."},{"key":"10.1016\/j.compbiomed.2023.106965_bib25","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1093\/clinids\/17.2.288","article-title":"Adverse neurological reactions in patients with multidrug-resistant pulmonary tuberculosis after coadministration of cycloserine and ofloxacin","volume":"17","author":"Yew","year":"1993","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.compbiomed.2023.106965_bib26","doi-asserted-by":"crossref","first-page":"1150","DOI":"10.1111\/febs.12108","article-title":"Kinetic mechanism and inhibition of Mycobacterium tuberculosis D-alanine: D-alanine ligase by the antibiotic D-cycloserine","volume":"280","author":"Prosser","year":"2013","journal-title":"FEBS J."},{"key":"10.1016\/j.compbiomed.2023.106965_bib27","doi-asserted-by":"crossref","first-page":"8921","DOI":"10.1073\/pnas.150116497","article-title":"The molecular basis of vancomycin resistance in clinically relevant Enterococci: crystal structure of D-alanyl-D-lactate ligase (VanA)","volume":"97","author":"Roper","year":"2000","journal-title":"Proc. Natl. Acad. Sci. USA"},{"issue":"5","key":"10.1016\/j.compbiomed.2023.106965_bib28","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1016\/S0969-2126(00)00129-5","article-title":"Enzymes of vancomycin resistance: the structure of D-alanine-D-lactate ligase of naturally resistant Leuconostoc mesenteroides","volume":"8","author":"Kuzin","year":"2000","journal-title":"Structure"},{"issue":"5","key":"10.1016\/j.compbiomed.2023.106965_bib29","doi-asserted-by":"crossref","first-page":"1128","DOI":"10.1021\/acschemneuro.7b00490","article-title":"What contributes to serotonin-norepinephrine reuptake inhibitors' dual-targeting mechanism? The key role of transmembrane domain 6 in human serotonin and norepinephrine transporters revealed by molecular dynamics simulation","volume":"9","author":"Xue","year":"2018","journal-title":"ACS Chem. Neurosci."},{"issue":"9","key":"10.1016\/j.compbiomed.2023.106965_bib30","doi-asserted-by":"crossref","first-page":"5132","DOI":"10.1039\/C9CP05764A","article-title":"The binding mode of vilazodone in the human serotonin transporter elucidated by ligand docking and molecular dynamics simulations","volume":"22","author":"Zhang","year":"2020","journal-title":"Phys. Chem. Chem. Phys."},{"issue":"8","key":"10.1016\/j.compbiomed.2023.106965_bib31","doi-asserted-by":"crossref","first-page":"1354","DOI":"10.1038\/s41401-020-00541-z","article-title":"Subtype-selective mechanisms of negative allosteric modulators binding to group I metabotropic glutamate receptors","volume":"42","author":"Fu","year":"2021","journal-title":"Acta Pharmacol. Sin."},{"issue":"11","key":"10.1016\/j.compbiomed.2023.106965_bib32","doi-asserted-by":"crossref","first-page":"2013","DOI":"10.1021\/acschemneuro.1c00127","article-title":"Understanding the polypharmacological profiles of triple reuptake inhibitors by molecular simulation","volume":"12","author":"Tu","year":"2021","journal-title":"ACS Chem. Neurosci."},{"issue":"3","key":"10.1016\/j.compbiomed.2023.106965_bib33","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1021\/acschemneuro.1c00694","article-title":"Molecular mechanism for the allosteric inhibition of the human serotonin transporter by antidepressant escitalopram","volume":"13","author":"Xue","year":"2022","journal-title":"ACS Chem. Neurosci."},{"key":"10.1016\/j.compbiomed.2023.106965_bib34","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1128\/AAC.50.3.1067-1070.2006","article-title":"Enterococcus gallinarum N04-0414 harbors a VanD-type vancomycin resistance operon and does not contain a D-alanine: D-alanine 2 (ddl2) gene","volume":"50","author":"Boyd","year":"2006","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.compbiomed.2023.106965_bib35","doi-asserted-by":"crossref","first-page":"1162","DOI":"10.1126\/science.252.5009.1162","article-title":"Predicting coiled coils from protein sequences","volume":"252","author":"Lupas","year":"1991","journal-title":"Science"},{"key":"10.1016\/j.compbiomed.2023.106965_bib36","doi-asserted-by":"crossref","first-page":"2138","DOI":"10.1093\/bioinformatics\/bth195","article-title":"The DISOPRED server for the prediction of protein disorder","volume":"20","author":"Ward","year":"2004","journal-title":"Bioinformatics"},{"key":"10.1016\/j.compbiomed.2023.106965_bib37","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes","volume":"305","author":"Krogh","year":"2001","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.compbiomed.2023.106965_bib38","doi-asserted-by":"crossref","first-page":"261","DOI":"10.18388\/abp.2008_3073","article-title":"Prediction of signal peptides in protein sequences by neural networks","volume":"55","author":"Plewczynski","year":"2008","journal-title":"Acta Biochim. Pol."},{"key":"10.1016\/j.compbiomed.2023.106965_bib39","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/0097-8485(94)85023-2","article-title":"Non-globular domains in protein sequences: automated segmentation using complexity measures","volume":"18","author":"Wootton","year":"1994","journal-title":"Comput. Chem."},{"key":"10.1016\/j.compbiomed.2023.106965_bib40","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1006\/jmbi.1999.3091","article-title":"Protein secondary structure prediction based on position-specific scoring matrices","volume":"292","author":"Jones","year":"1999","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.compbiomed.2023.106965_bib41","first-page":"531","article-title":"Protein identification, and analysis tools in the ExPASy server","volume":"112","author":"Wilkins","year":"1999","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.compbiomed.2023.106965_bib42","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiomed.2023.106965_bib43","first-page":"899","article-title":"The protein Data Bank","volume":"58","author":"Berman","year":"2002","journal-title":"Acta Crystallogr."},{"key":"10.1016\/j.compbiomed.2023.106965_bib44","doi-asserted-by":"crossref","first-page":"5465","DOI":"10.1128\/JB.00613-10","article-title":"Molecular basis of vancomycin dependence in VanA-type Staphylococcus aureus VRSA-9","volume":"192","author":"Meziane-Cherif","year":"2010","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.compbiomed.2023.106965_bib45","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1128\/AAC.00558-10","article-title":"Structure of the Mycobacterium tuberculosis D-alanine: D-alanine ligase, a target of the antituberculosis drug D-cycloserine","volume":"55","author":"Bruning","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"issue":"24","key":"10.1016\/j.compbiomed.2023.106965_bib46","doi-asserted-by":"crossref","first-page":"4876","DOI":"10.1093\/nar\/25.24.4876","article-title":"The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools","volume":"25","author":"Thompson","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiomed.2023.106965_bib47","doi-asserted-by":"crossref","first-page":"W320","DOI":"10.1093\/nar\/gku316","article-title":"Deciphering key features in protein structures with the new ENDscript server","volume":"42","author":"Robert","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiomed.2023.106965_bib48","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1006\/jmbi.1993.1626","article-title":"Comparative protein modelling by satisfaction of spatial restraints","volume":"234","author":"Sali","year":"1993","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.compbiomed.2023.106965_bib49","doi-asserted-by":"crossref","first-page":"2525","DOI":"10.1016\/j.bpj.2011.10.024","article-title":"Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization","volume":"101","author":"Xu","year":"2011","journal-title":"Biophys. J."},{"key":"10.1016\/j.compbiomed.2023.106965_bib50","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1107\/S0021889892009944","article-title":"PROCHECK: a program to check the stereochemical quality of protein structures","volume":"26","author":"Laskowski","year":"1993","journal-title":"J. Appl. Crystallogr."},{"key":"10.1016\/j.compbiomed.2023.106965_bib51","doi-asserted-by":"crossref","first-page":"W407","DOI":"10.1093\/nar\/gkm290","article-title":"ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins","volume":"35","author":"Wiederstein","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiomed.2023.106965_bib52","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1126\/science.1853201","article-title":"A method to identify protein sequences that fold into a known three-dimensional structure","volume":"253","author":"Bowie","year":"1991","journal-title":"Science"},{"key":"10.1016\/j.compbiomed.2023.106965_bib53","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera--a visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.compbiomed.2023.106965_bib54","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"Gromacs: high-performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1\u20132","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"10.1016\/j.compbiomed.2023.106965_bib55","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.2023.106965_bib56","doi-asserted-by":"crossref","first-page":"W314","DOI":"10.1093\/nar\/gkt503","article-title":"Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins","volume":"41","author":"Tan","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiomed.2023.106965_bib57","doi-asserted-by":"crossref","first-page":"2785","DOI":"10.1002\/jcc.21256","article-title":"AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility","volume":"30","author":"Morris","year":"2009","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.compbiomed.2023.106965_bib58","doi-asserted-by":"crossref","first-page":"D1202","DOI":"10.1093\/nar\/gkv951","article-title":"PubChem substance and compound databases","volume":"44","author":"Kim","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiomed.2023.106965_bib59","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0169-409X(00)00129-0","article-title":"Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings","volume":"46","author":"Lipinski","year":"2001","journal-title":"Adv. Drug Deliv. Rev."},{"key":"10.1016\/j.compbiomed.2023.106965_bib60","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","volume":"7","author":"Daina","year":"2017","journal-title":"Sci. Rep."},{"issue":"8","key":"10.1016\/j.compbiomed.2023.106965_bib61","doi-asserted-by":"crossref","first-page":"3917","DOI":"10.1021\/acs.jcim.1c00355","article-title":"Structure-based discovery of novel nonpeptide inhibitors targeting SARS-CoV-2 Mpro","volume":"61","author":"Yang","year":"2021","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/j.compbiomed.2023.106965_bib62","doi-asserted-by":"crossref","first-page":"3099","DOI":"10.1021\/ci300367a","article-title":"admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties","volume":"52","author":"Cheng","year":"2012","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/j.compbiomed.2023.106965_bib63","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1758-2946-3-33","article-title":"Open Babel: an open chemical toolbox","volume":"3","author":"O'Boyle","year":"2011","journal-title":"J. Cheminf."},{"key":"10.1016\/j.compbiomed.2023.106965_bib64","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera - a visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.compbiomed.2023.106965_bib65","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13321-015-0109-z","article-title":"ChemDes : an integrated web-based platform for molecular descriptor and fingerprint computation","volume":"7","author":"Dong","year":"2015","journal-title":"J. Cheminf."},{"key":"10.1016\/j.compbiomed.2023.106965_bib66","doi-asserted-by":"crossref","first-page":"998","DOI":"10.1021\/ja01489a058","article-title":"Competitive inhibition of enzymatic reactions by oxamycin","volume":"82","author":"Strominger","year":"1960","journal-title":"J. Am. Chem. Soc."},{"key":"10.1016\/j.compbiomed.2023.106965_bib67","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1007\/s10989-014-9434-8","article-title":"Identification of angiotensin converting enzyme inhibitor: an in silico perspective","volume":"21","author":"Jalkute","year":"2015","journal-title":"Int. J. Pept. Res. Therapeut."},{"key":"10.1016\/j.compbiomed.2023.106965_bib68","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1002\/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B","article-title":"Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function","volume":"19","author":"Morris","year":"1998","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.compbiomed.2023.106965_bib69","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1007\/s10930-013-9492-3","article-title":"Molecular dynamics simulation and molecular docking studies of angiotensin converting enzyme with inhibitor lisinopril and amyloid beta peptide","volume":"32","author":"Jalkute","year":"2013","journal-title":"Protein J."},{"key":"10.1016\/j.compbiomed.2023.106965_bib70","doi-asserted-by":"crossref","first-page":"2679","DOI":"10.1002\/jcb.26435","article-title":"Molecular modeling studies to explore the binding affinity of virtually screened inhibitor toward different aminoglycoside kinases from diverse MDR strains","volume":"119","author":"Parulekar","year":"2018","journal-title":"J. Cell. Biochem."},{"key":"10.1016\/j.compbiomed.2023.106965_bib71","doi-asserted-by":"crossref","first-page":"892","DOI":"10.1021\/acsomega.8b02672","article-title":"Molecular insights into destabilization of alzheimer's a\u03b2 protofibril by arginine containing short peptides: a molecular modeling approach","volume":"4","author":"Barale","year":"2019","journal-title":"ACS Omega"},{"key":"10.1016\/j.compbiomed.2023.106965_bib72","doi-asserted-by":"crossref","DOI":"10.1016\/j.imu.2021.100597","article-title":"Structural insights and inhibition mechanism of TMPRSS2 by experimentally known inhibitors Camostat mesylate, Nafamostat and Bromhexine hydrochloride to control SARS-coronavirus-2: a molecular modeling approach","volume":"24","author":"Sonawane","year":"2021","journal-title":"Inform. Med. Unlocked"},{"key":"10.1016\/j.compbiomed.2023.106965_bib73","doi-asserted-by":"crossref","first-page":"6474","DOI":"10.1021\/jp003919d","article-title":"Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides","volume":"105","author":"Kaminski","year":"2001","journal-title":"J. Phys. Chem. B"},{"key":"10.1016\/j.compbiomed.2023.106965_bib74","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1021\/ct700200b","article-title":"P-LINCS: a parallel linear Constraint solver for molecular simulation","volume":"4","author":"Hess","year":"2008","journal-title":"J. Chem. Theor. Comput."},{"key":"10.1016\/j.compbiomed.2023.106965_bib75","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1063\/1.470117","article-title":"A smooth particle mesh Ewald method","volume":"103","author":"Essmann","year":"1995","journal-title":"J. Chem. Phys."},{"key":"10.1016\/j.compbiomed.2023.106965_bib76","doi-asserted-by":"crossref","DOI":"10.1063\/1.2408420","article-title":"Canonical sampling through velocity rescaling","volume":"126","author":"Bussi","year":"2007","journal-title":"J. Chem. Phys."},{"key":"10.1016\/j.compbiomed.2023.106965_bib77","doi-asserted-by":"crossref","first-page":"3684","DOI":"10.1063\/1.448118","article-title":"Molecular dynamics with coupling to an external bath","volume":"81","author":"Berendsen","year":"1984","journal-title":"J. Chem. Phys."},{"key":"10.1016\/j.compbiomed.2023.106965_bib78","doi-asserted-by":"crossref","first-page":"5834","DOI":"10.1021\/acs.jctc.8b00768","article-title":"Automated topology builder version 3.0: prediction of solvation free enthalpies in water and hexane","volume":"14","author":"Koen","year":"2018","journal-title":"J. Chem. Theor. Comput."},{"key":"10.1016\/j.compbiomed.2023.106965_bib79","doi-asserted-by":"crossref","first-page":"1951","DOI":"10.1021\/ci500020m","article-title":"G-mmpbsa -A GROMACS tool for high-throughput MM-PBSA calculations","volume":"54","author":"Kumari","year":"2014","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/j.compbiomed.2023.106965_bib80","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1002\/prot.340170408","article-title":"Essential dynamics of proteins","volume":"17","author":"Amadei","year":"1993","journal-title":"Proteins"},{"key":"10.1016\/j.compbiomed.2023.106965_bib81","doi-asserted-by":"crossref","first-page":"1712","DOI":"10.1038\/s41598-022-05698-7","article-title":"Identification of novel leads as potent inhibitors of HDAC3 using ligand-based pharmacophore modeling and MD simulation","volume":"12","author":"Kumbhar","year":"2022","journal-title":"Sci. Rep."},{"issue":"24","key":"10.1016\/j.compbiomed.2023.106965_bib82","doi-asserted-by":"crossref","first-page":"3403","DOI":"10.1093\/bioinformatics\/btm477","article-title":"XtalPred: a web server for the prediction of protein crystallizability","volume":"23","author":"Slabinski","year":"2007","journal-title":"Bioinformatics"},{"year":"2005","series-title":"The Proteomics Protocols Handbook","author":"Gasteiger","key":"10.1016\/j.compbiomed.2023.106965_bib83"},{"key":"10.1016\/j.compbiomed.2023.106965_bib84","doi-asserted-by":"crossref","first-page":"2860","DOI":"10.1093\/bioinformatics\/bth300","article-title":"TargetDB : a target registration database for structural genomics projects","volume":"20","author":"Chen","year":"2004","journal-title":"Bioinformatics"},{"key":"10.1016\/j.compbiomed.2023.106965_bib85","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/356083a0","article-title":"Assessment of protein models with three-dimensional profiles","volume":"356","author":"L\u00fcthy","year":"1992","journal-title":"Nature"},{"key":"10.1016\/j.compbiomed.2023.106965_bib86","doi-asserted-by":"crossref","first-page":"7145","DOI":"10.1021\/bi400839f","article-title":"Reinterpreting the mechanism of inhibition of Mycobacterium tuberculosis d-Alanine:d-Alanine ligase by d-cycloserine","volume":"52","author":"Prosser","year":"2013","journal-title":"Biochemistry"},{"key":"10.1016\/j.compbiomed.2023.106965_bib87","doi-asserted-by":"crossref","first-page":"1098","DOI":"10.1107\/S0907444909029710","article-title":"Structure of D-alanine-D-alanine ligase from Thermus thermophilus HB8: cumulative conformational change and enzyme-ligand interactions","volume":"65","author":"Kitamura","year":"2009","journal-title":"Acta. Crystallogr. D. Biol. Crystallogr."},{"key":"10.1016\/j.compbiomed.2023.106965_bib88","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1016\/j.abb.2014.01.009","article-title":"Crystal structures of d-alanine-d-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides","volume":"545","author":"Doan","year":"2014","journal-title":"Arch. Biochem. Biophys."},{"key":"10.1016\/j.compbiomed.2023.106965_bib89","doi-asserted-by":"crossref","first-page":"14006","DOI":"10.1021\/bi991384c","article-title":"Determinants for differential effects on D-Ala-D-lactate vs D-Ala-D-Ala formation by the VanA ligase from vancomycin-resistant enterococci","volume":"38","author":"Lessard","year":"1999","journal-title":"Biochemistry"},{"key":"10.1016\/j.compbiomed.2023.106965_bib90","doi-asserted-by":"crossref","first-page":"9210","DOI":"10.1074\/jbc.272.14.9210","article-title":"D-Alanyl-D-lactate and D-alanyl-D-alanine synthesis by D-alanyl-D-alanine ligase from vancomycin-resistant Leuconostoc mesenteroides. Effects of a phenylalanine 261 to tyrosine mutation","volume":"272","author":"Park","year":"1997","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.compbiomed.2023.106965_bib91","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1016\/j.jmgm.2010.01.010","article-title":"Role of Arg301 in substrate orientation and catalysis in subsite 2 of d-alanine:d-alanine (d-lactate) ligase from Leuconostoc mesenteroides: a molecular docking study","volume":"28","author":"Neuhaus","year":"2010","journal-title":"J. Mol. Graph. Model."},{"key":"10.1016\/j.compbiomed.2023.106965_bib92","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.jmgm.2011.06.002","article-title":"Role of the omega loop in specificity determination in subsite 2 of the d -alanine : D -alanine (d -lactate) ligase from Leuconostoc mesenteroides : a molecular docking study","volume":"30","author":"Neuhaus","year":"2011","journal-title":"J. Mol. Graph. Model."},{"issue":"15","key":"10.1016\/j.compbiomed.2023.106965_bib93","doi-asserted-by":"crossref","first-page":"6849","DOI":"10.1021\/jm3006965","article-title":"Function of the D -alanine: D -alanine ligase lid loop: a molecular modeling and bioactivity study","volume":"55","author":"Hrast","year":"2012","journal-title":"J. Med. Chem."},{"key":"10.1016\/j.compbiomed.2023.106965_bib94","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1107\/S2059798315021671","article-title":"Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop","volume":"72","author":"Tran","year":"2016","journal-title":"Acta. Crystallogr. D. Struct. Biol."},{"key":"10.1016\/j.compbiomed.2023.106965_bib95","doi-asserted-by":"crossref","first-page":"1762","DOI":"10.1021\/acs.jcim.6b00211","article-title":"Building graphs to describe dynamics, kinetics, and energetics in the d-Ala:d-Lac ligase VanA","volume":"56","author":"Duclert-Savatier","year":"2016","journal-title":"J. Chem. Inf. Model."}],"container-title":["Computers in Biology and Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0010482523004304?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0010482523004304?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,1,9]],"date-time":"2025-01-09T00:19:54Z","timestamp":1736381994000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0010482523004304"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,6]]},"references-count":95,"alternative-id":["S0010482523004304"],"URL":"https:\/\/doi.org\/10.1016\/j.compbiomed.2023.106965","relation":{},"ISSN":["0010-4825"],"issn-type":[{"type":"print","value":"0010-4825"}],"subject":[],"published":{"date-parts":[[2023,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Structure based virtual screening, molecular dynamic simulation to identify the oxadiazole derivatives as inhibitors of Enterococcus D-Ala-D-Ser ligase for combating vancomycin resistance","name":"articletitle","label":"Article Title"},{"value":"Computers in Biology and Medicine","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.compbiomed.2023.106965","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 Elsevier Ltd. All rights reserved.","name":"copyright","label":"Copyright"}],"article-number":"106965"}}