{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T10:35:48Z","timestamp":1772793348401,"version":"3.50.1"},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2009,5,30]],"date-time":"2009-05-30T00:00:00Z","timestamp":1243641600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Mol Model"],"published-print":{"date-parts":[[2010,1]]},"DOI":"10.1007\/s00894-009-0521-2","type":"journal-article","created":{"date-parts":[[2009,5,29]],"date-time":"2009-05-29T13:03:56Z","timestamp":1243602236000},"page":"77-85","source":"Crossref","is-referenced-by-count":18,"title":["Probing ligand binding modes of Mycobacterium tuberculosis MurC ligase by molecular modeling, dynamics simulation and docking"],"prefix":"10.1007","volume":"16","author":[{"given":"C. M.","family":"Anuradha","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chaitanya","family":"Mulakayala","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Banaganapalli","family":"Babajan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M.","family":"Naveen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chikati","family":"Rajasekhar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chitta Suresh","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,5,30]]},"reference":[{"key":"521_CR1","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1126\/science.257.5073.1055","volume":"257","author":"BR Bloom","year":"1992","unstructured":"Bloom BR, Murray CJ (1992) Tuberculosis: Commentary on a reemergent killer. Science 257:1055\u20131064","journal-title":"Science"},{"key":"521_CR2","unstructured":"World Health Organization. Anti-tuberculosis Drug Resistance in the World. Report No.2. The WHO\/IUATLD Global Project on Anti-tuberculosis Drug Resistance Surveillance. WHO, Geneva, Switzerland. 1997\u20132000"},{"key":"521_CR3","first-page":"1","volume":"117","author":"P Chopra","year":"2003","unstructured":"Chopra P, Meena LS, Sing Y (2003) New Drug-targets for Mycobacterium Tuberculosis. Indian J Med Res 117:1\u20139","journal-title":"Indian J Med Res"},{"key":"521_CR4","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1164\/ajrccm.163.5.2007122","volume":"163","author":"RJ O\u2019Brien","year":"2001","unstructured":"O\u2019Brien RJ, Nunn PP (2001) The need for new drugs against tuberculosis. Obstacles. Opportunities and next steps. Am J Respir Crit Care Med 163:1055\u20131058","journal-title":"Am J Respir Crit Care Med"},{"key":"521_CR5","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1016\/j.compbiolchem.2005.07.001","volume":"29","author":"A Sharmila","year":"2005","unstructured":"Sharmila A, Mrudula P, Gautam P (2005) Potential drug targets in Mycobacterium Tuberculosis through metabolic pathway analysis. Comput Biol Chem 29:368\u2013378","journal-title":"Comput Biol Chem"},{"key":"521_CR6","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/S0065-2911(08)60016-8","volume":"39","author":"M Daffe","year":"1998","unstructured":"Daffe M, Draper P (1998) The envelope layers of mycobacteria with reference to their pathogenicity. Adv Microbiol Physiol 39:131\u2013203","journal-title":"Adv Microbiol Physiology"},{"key":"521_CR7","doi-asserted-by":"crossref","first-page":"1253","DOI":"10.2741\/A360","volume":"3","author":"P Draper","year":"1998","unstructured":"Draper P (1998) The outer parts of mycobacterial envelope as permeability barriers. Front Biosci 3:1253\u20131261 PMID:9851911","journal-title":"Front Biosci"},{"key":"521_CR8","doi-asserted-by":"crossref","first-page":"11561","DOI":"10.1046\/j.1365-2958.1999.01304.x","volume":"31","author":"H Christensen","year":"1999","unstructured":"Christensen H, Garton NJ, Horobin RW, Minnikin DE, Barer MR (1999) Lipid domains of Mycobacteria Studied with fluorescent molecular probes. Mol Microbiol 31:11561\u201311572","journal-title":"Mol Microbiol"},{"key":"521_CR9","first-page":"154","volume":"2","author":"DC Crick","year":"2000","unstructured":"Crick DC, Brennan PJ (2000) Antituberculosis drug research. Curr Opin Anti-infect Investig Drugs 2:154\u2013163","journal-title":"Curr Opin Anti-infect Investig Drugs"},{"key":"521_CR10","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1039\/a804532a","volume":"18","author":"J Heijeinoot Van","year":"2001","unstructured":"Van Heijeinoot J (2001) Recent advances in the formation of bacterial peptidoglycan monomer unit. Nat Prod Rep 18:503\u2013519","journal-title":"Nat Prod Rep"},{"key":"521_CR11","unstructured":"NCBI. http:\/\/www.ncbi.nlm.nih.gov\/"},{"key":"521_CR12","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altshul","year":"1997","unstructured":"Altshul SF, Madden TL, Schaffer AA, Zhang J, Zhang W, Mille W, Lipman D (1997) Gapped Blast and PSI BLAST: a new generation of protein data base search programs. J Nucl Acids Res 25:3389\u20133402","journal-title":"J Nucl Acids Res"},{"key":"521_CR13","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucl Acids Res 28:235\u2013242","journal-title":"Nucl Acids Res"},{"key":"521_CR14","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","volume":"22","author":"JD Thompson","year":"1994","unstructured":"Thompson JD, Higgins DG, Gibson TJ (1994) Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting position- specific gap penalties and weight matrix choice. Nucl Acids Res 22:4673\u20134680","journal-title":"Nucl Acids Res"},{"key":"521_CR15","unstructured":"http:\/\/www.salilab.org\/modeller\/9v3"},{"key":"521_CR16","doi-asserted-by":"crossref","first-page":"2714","DOI":"10.1002\/elps.1150181505","volume":"18","author":"N Guex","year":"1997","unstructured":"Guex N, Peitsch MC (1997) SWISS MODEL and the Swiss pdb viewer: an environment for comparative protein modeling. Electrophoresis 18:2714\u20132723","journal-title":"Electrophoresis"},{"key":"521_CR17","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1007\/s008940100045","volume":"7","author":"E Lindal","year":"2001","unstructured":"Lindal E, Hess B, Van der Spoel D (2001) Gromacs 3.0: A package for molecular simulation and trajectory analysis. J Mol Model 7:306\u2013317","journal-title":"J Mol Model"},{"key":"521_CR18","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1007\/978-94-015-7658-1_21","volume-title":"Intermolecular Forces","author":"HJC Berendsen","year":"1981","unstructured":"Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J (1981) Interaction models for water in relation to protein hydration. In: Pullman B (ed) Intermolecular Forces. Reidel, Dordrecht, pp 331\u2013342"},{"key":"521_CR19","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","volume":"18","author":"B Hess","year":"1997","unstructured":"Hess B, Bekker H, Berendsen HJC, Freeije JGEM (1997) LINICS: A linear constraint solver for molecular simulations. J Comput Chem 18:1463\u20131472","journal-title":"J Comput Chem"},{"key":"521_CR20","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1002\/jcc.540130805","volume":"13","author":"S Miyamoto","year":"1992","unstructured":"Miyamoto S, Kollman PA (1992) SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models. J Comput Chem 13:952\u2013962","journal-title":"J Comput Chem"},{"key":"521_CR21","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1107\/S0021889892009944","volume":"26","author":"RA Laskowski","year":"1993","unstructured":"Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK a program to check the stereo chemical quality of protein structure. J Appl Cryst 26:283\u2013291","journal-title":"J Appl Cryst"},{"key":"521_CR22","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/0263-7855(90)80070-V","volume":"8","author":"G Vriend","year":"1990","unstructured":"Vriend G (1990) WHATIF: a molecular modeling and drug design program. J Mol Graph\u00a08:52\u201356","journal-title":"J Mol Graph"},{"key":"521_CR23","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1002\/prot.340170404","volume":"17","author":"MJ Sippl","year":"1993","unstructured":"Sippl MJ (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17:355\u2013362","journal-title":"Proteins"},{"key":"521_CR24","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/356083a0","volume":"356","author":"R Luthy","year":"1992","unstructured":"Luthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356:83\u201385","journal-title":"Nature"},{"key":"521_CR25","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1126\/science.1853201","volume":"253","author":"JU Bowie","year":"1991","unstructured":"Bowie JU, Luthy R, Eisenberg D (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253:164\u2013170","journal-title":"Science"},{"key":"521_CR26","doi-asserted-by":"crossref","first-page":"W63","DOI":"10.1093\/nar\/gkl341","volume":"34","author":"MV Berjanskii","year":"2006","unstructured":"Berjanskii MV, Neal S, Wishart DS (2006) PREDITOR: a web server for predicting protein torsion angle restraints. Nucl Acids Res 34:W63\u2013W69","journal-title":"Nucl Acids Res"},{"key":"521_CR27","doi-asserted-by":"crossref","first-page":"W89","DOI":"10.1093\/nar\/gki414","volume":"33","author":"RA Laskowski","year":"2005","unstructured":"Laskowski RA, Watson JD, Thornton JM (2005) ProFunc: a server for predicting protein function from 3D structure. Nucl Acids Res 33:W89\u2013W93","journal-title":"Nucl Acids Res"},{"issue":"6","key":"521_CR28","doi-asserted-by":"crossref","first-page":"1505","DOI":"10.1021\/ci025575p","volume":"42","author":"RE Buntrock","year":"2002","unstructured":"Buntrock RE (2002) ChemOffice Ultra 7.0. J Chem Inf Comput Sci 42(6):1505\u20131506 http:\/\/www.molinspiration.com","journal-title":"J Chem Inf Comput Sci"},{"key":"521_CR29","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0169-409X(00)00129-0","volume":"46","author":"CA Lipinski","year":"2001","unstructured":"Lipinski CA, Lombardo F, Dominy W, Feeney PJ (2001) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 46:3\u201326","journal-title":"Adv Drug Deliv Rev"},{"issue":"14","key":"521_CR30","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1002\/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B","volume":"19","author":"DS Goodsell","year":"1998","unstructured":"Goodsell DS, Morris GM (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19(14):1639\u20131662","journal-title":"J Comput Chem"},{"key":"521_CR31","doi-asserted-by":"crossref","first-page":"1308","DOI":"10.1021\/ci010366a","volume":"41","author":"TI Oprea","year":"2001","unstructured":"Oprea TI, Davis AM, Teague SJ, Leeson PD (2001) Is there a Difference between Leads and Drugs? A Historical Perspective. J Chem Inf Comput Sci 41:1308\u20131315","journal-title":"J Chem Inf Comput Sci"},{"key":"521_CR32","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1093\/nar\/gkj105","volume":"34","author":"T Castrignano","year":"2006","unstructured":"Castrignano T, De Meo PDO, Ozzetto D et al (2006) The PMBD Protein Model Database. Nucl Acids Res 34:306\u2013309","journal-title":"Nucl Acids Res"},{"key":"521_CR33","doi-asserted-by":"crossref","first-page":"4152","DOI":"10.1128\/JB.185.14.4152-4162.2003","volume":"185","author":"CD Mol","year":"2003","unstructured":"Mol CD, Broom AA, Dougan DR, Hilgers MT, Tari TW, Wijnands AA, Knuth MW, McCrae DE, Swanson RV (2003) Crystal Structure of Active of fully assembled Substrate & Product bound complexes of UDP-N-Acetyl muramic acid: L-Alanine Ligase (MurC) from Haemophilus influenza. J Bacteriol 185:4152\u20134162","journal-title":"J Bacteriol"},{"key":"521_CR34","unstructured":"Skarzynski T, Cleasby A, Domenici E, Gevi M, Shaw J (in press) Crystal Structure of UDP-N-Acetyl muramic acid: L-Alanine Ligase (MurC) from Haemophilus influenzae."}],"container-title":["Journal of Molecular Modeling"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-009-0521-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s00894-009-0521-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-009-0521-2","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,29]],"date-time":"2019-05-29T02:51:54Z","timestamp":1559098314000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s00894-009-0521-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,5,30]]},"references-count":34,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,1]]}},"alternative-id":["521"],"URL":"https:\/\/doi.org\/10.1007\/s00894-009-0521-2","relation":{},"ISSN":["1610-2940","0948-5023"],"issn-type":[{"value":"1610-2940","type":"print"},{"value":"0948-5023","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,5,30]]}}}