{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T12:09:00Z","timestamp":1791202140987,"version":"4.2.0"},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2011,3,29]],"date-time":"2011-03-29T00:00:00Z","timestamp":1301356800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2011,3,29]],"date-time":"2011-03-29T00:00:00Z","timestamp":1301356800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Mol Model"],"published-print":{"date-parts":[[2012,1]]},"DOI":"10.1007\/s00894-011-1018-3","type":"journal-article","created":{"date-parts":[[2011,3,28]],"date-time":"2011-03-28T22:14:49Z","timestamp":1301350489000},"page":"39-51","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":82,"title":["Homology modeling, molecular dynamics, e-pharmacophore mapping and docking study of Chikungunya virus nsP2 protease"],"prefix":"10.1007","volume":"18","author":[{"given":"Kh. Dhanachandra","family":"Singh","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Palani","family":"Kirubakaran","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shanthi","family":"Nagarajan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sugunadevi","family":"Sakkiah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karthikeyan","family":"Muthusamy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Devadasan","family":"Velmurgan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeyaraman","family":"Jeyakanthan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2011,3,29]]},"reference":[{"key":"1018_CR1","doi-asserted-by":"crossref","first-page":"804","DOI":"10.1371\/journal.ppat.0030089","volume":"3","author":"M Sourisseau","year":"2007","unstructured":"Sourisseau M, Schilte C, Casartelli N, Trouillet C, Guivel-Benhassine F, Rudnicka D, Sol-Foulon N, Roux KL, Prevost M-C, Fsihi H, Frenkiel M-P, Blanchet F, Afonso PV, Ceccaldi P-E, Ozden S, Gessain A, Schuffenecker I, Verhasselt B, Zamborlini A, Saib A, Rey FA, Arenzana-Seisdedos F, Despres P, Michault A, Albert ML, Schwartz O (2007) Characterization of reemerging Chikungunya virus. PLoS Pathog 3:804\u2013817","journal-title":"PLoS Pathog"},{"key":"1018_CR2","doi-asserted-by":"publisher","first-page":"1058","DOI":"10.1371\/journal.pmed.0030263","volume":"3","author":"I Schuffenecker","year":"2006","unstructured":"Schuffenecker I, Iteman I, Michault A, Murri S, Frangeul L, Vaney M-C, Lavenir R, Pardigon N, Reynes J-M, Pettinelli F, Biscornet L, Diancourt L, Michel S, Duquerroy S, Guigon G, Frenkiel M-P, Brhin A-C, Cubito N, Desprs P, Kunst F, Rey F, Zeller H, Brisse S (2006) Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak. PLoS Med 3:1058\u20131070","journal-title":"PLoS Med"},{"key":"1018_CR3","doi-asserted-by":"crossref","unstructured":"Ng LFP, Chow A, Sun YJ, Kwek DJC, Lim PL, Dimatatac F, Ng LC, Ooi EE, Choo KH, Her Z, Kourilsky P, Leo YS (2009) IL-\u03b2, IL-6, and RANTES as biomarkers of Chikungunya severity. PLoS ONE 4:e4261","DOI":"10.1371\/journal.pone.0004261"},{"key":"1018_CR4","doi-asserted-by":"crossref","first-page":"616","DOI":"10.4269\/ajtmh.2005.72.616","volume":"72","author":"DL Vanlandingham","year":"2005","unstructured":"Vanlandingham DL, Hong C, Klingler K, Tsetsarkin K, McElroy KL, Powers AM, Lehane MJ, Higgs S (2005) Differential infectivities of O\u2019nyong-nyong and Chikungunya virus isolates in anopheles gambiae and Aedes aegypti mosquitoes. Am J Trop Med Hyg 72:616\u2013621","journal-title":"Am J Trop Med Hyg"},{"key":"1018_CR5","doi-asserted-by":"crossref","first-page":"2921","DOI":"10.1002\/art.23753","volume":"58","author":"A Chopra","year":"2008","unstructured":"Chopra A, Anuradha V, Lagoo-Joshi V, Kunjir V, Salvi S, Saluja M (2008) Chikungunya virus aches and pains: an emerging challenge. Arthritis Rheum 58:2921\u20132922","journal-title":"Arthritis Rheum"},{"key":"1018_CR6","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.patbio.2008.02.016","volume":"57","author":"N Pardigon","year":"2009","unstructured":"Pardigon N (2009) The biology of chikungunya: a brief review of what we still do not know. Pathol Biol 57:127\u2013132","journal-title":"Pathol Biol"},{"key":"1018_CR7","doi-asserted-by":"publisher","first-page":"5667","DOI":"10.1093\/nar\/14.14.5667","volume":"14","author":"K Takkinen","year":"1986","unstructured":"Takkinen K (1986) Complete nucleotide sequence of the nonstructural protein genes of Semliki Forest virus. Nucleic Acids Res 14:5667\u20135682","journal-title":"Nucleic Acids Res"},{"key":"1018_CR8","doi-asserted-by":"crossref","first-page":"3075","DOI":"10.1099\/0022-1317-83-12-3075","volume":"83","author":"AH Khan","year":"2002","unstructured":"Khan AH, Morita K, MdC P, Hasebe F, Mathenge EGM, Igarashi A (2002) Complete nucleotide sequence of Chikungunya virus and evidence for an internal polyadenylation site. J Gen Virol 83:3075\u20133084","journal-title":"J Gen Virol"},{"key":"1018_CR9","doi-asserted-by":"crossref","unstructured":"Strauss EGS, Strauss JH (1986) Structure and replication of the alphavirus genome. The Togaviridae and Flaviridae. Plenum, New York, pp 35\u201390","DOI":"10.1007\/978-1-4757-0785-4_3"},{"key":"1018_CR10","doi-asserted-by":"crossref","first-page":"5413","DOI":"10.1128\/JVI.00229-06","volume":"80","author":"A Lulla","year":"2006","unstructured":"Lulla A, Lulla V, Tints K, Ahola T, Merits A (2006) Molecular determinants of substrate specificity for Semliki Forest virus nonstructural protease. J Virol 80:5413\u20135422","journal-title":"J Virol"},{"key":"1018_CR11","doi-asserted-by":"crossref","first-page":"9802","DOI":"10.1128\/JVI.74.20.9802-9807.2000","volume":"74","author":"S Perri","year":"2000","unstructured":"Perri S, Driver DA, Gardner JP, Sherrill S, Belli BA, Dubensky TW Jr, Polo JM (2000) Replicon vectors derived from Sindbis virus and Semliki Forest virus that establish persistent replication in host cells. J Virol 74:9802\u20139807","journal-title":"J Virol"},{"key":"1018_CR12","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1016\/j.pep.2008.10.013","volume":"64","author":"D Zhang","year":"2009","unstructured":"Zhang D, T\u00f6zs\u00e9r J, Waugh DS (2009) Molecular cloning, overproduction, purification and biochemical characterization of the p39 nsp2 protease domains encoded by three alphaviruses. Protein Expr Purif 64:89\u201397","journal-title":"Protein Expr Purif"},{"key":"1018_CR13","doi-asserted-by":"crossref","first-page":"17281","DOI":"10.1074\/jbc.M910340199","volume":"275","author":"L Vasiljeva","year":"2000","unstructured":"Vasiljeva L, Merits A, Auvinen P, Kaariainen L (2000) Identification of a novel function of the alphavirus capping apparatus. J Biol Chem 275:17281\u201317287","journal-title":"J Biol Chem"},{"key":"1018_CR14","doi-asserted-by":"crossref","first-page":"2475","DOI":"10.1021\/jp952190j","volume":"100","author":"L Li","year":"1996","unstructured":"Li L, Darden T, Hiskey R, Pedersen L (1996) Homology modeling and molecular dynamics simulations of the Gla domains of human coagulation factor IX and its G[12]A mutant. J Phys Chem 100:2475\u20132479","journal-title":"J Phys Chem"},{"key":"1018_CR15","unstructured":"Kevin JB, Edmond C, Huafeng X, Ron OD, Michael PE, Brent AG, John LK, Istvan K, Mark AM, Federico DS, John KS, Yibing S, David ES (2006) Scalable algorithms for molecular dynamics simulations on commodity clusters. In: Proceedings of the 2006 ACM\/IEEE Conference on Supercomputing. ACM, Tampa"},{"key":"1018_CR16","doi-asserted-by":"publisher","first-page":"1318","DOI":"10.1002\/jcc.20267","volume":"26","author":"DE Shaw","year":"2005","unstructured":"Shaw DE (2005) A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. J Comput Chem 26:1318\u20131328","journal-title":"J Comput Chem"},{"key":"1018_CR17","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1093\/bib\/5.1.39","volume":"5","author":"A Bairoch","year":"2004","unstructured":"Bairoch A, Boeckmann B, Ferro S, Gasteiger E (2004) Swiss-Prot: juggling between evolution and stability. Brief Bioinform 5:39\u201355","journal-title":"Brief Bioinform"},{"key":"1018_CR18","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389\u20133402","journal-title":"Nucleic Acids Res"},{"key":"1018_CR19","doi-asserted-by":"crossref","first-page":"1449","DOI":"10.1016\/j.str.2006.07.010","volume":"14","author":"AT Russo","year":"2006","unstructured":"Russo AT, White MA, Watowich SJ (2006) The crystal structure of the Venezuelan equine encephalitis alphavirus nsP2 protease. Structure\u00a014:1449\u20131458","journal-title":"Structure"},{"key":"1018_CR20","unstructured":"Schr\u00f6dinger, LLC (2009) Prime, version 2.1. Schr\u00f6dinger, LLC, New York"},{"key":"1018_CR21","doi-asserted-by":"crossref","first-page":"11225","DOI":"10.1021\/ja9621760","volume":"118","author":"WL Jorgensen","year":"1996","unstructured":"Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225\u201311236","journal-title":"J Am Chem Soc"},{"key":"1018_CR22","doi-asserted-by":"publisher","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 stereochemical quality of protein structures. J Appl Crystallogr 26:283\u2013291","journal-title":"J Appl Crystallogr"},{"key":"1018_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 Struct Funct Bioinf 17:355\u2013362","journal-title":"Proteins Struct Funct Bioinf"},{"key":"1018_CR24","unstructured":"PyMOL (2010) PyMOL molecular graphics system website. http:\/\/www.pymol.org, accessed 2010"},{"key":"1018_CR25","doi-asserted-by":"publisher","first-page":"184109","DOI":"10.1063\/1.2191489","volume":"124","author":"KJ Bowers","year":"2006","unstructured":"Bowers KJ, Dror RO, Shaw DE (2006) The midpoint method for parallelization of particle simulations. J Chem Phys 124:184109\u2013184111","journal-title":"J Chem Phys"},{"key":"1018_CR26","doi-asserted-by":"crossref","first-page":"6474","DOI":"10.1021\/jp003919d","volume":"105","author":"GA Kaminski","year":"2001","unstructured":"Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL (2001) Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 105:6474\u20136487","journal-title":"J Phys Chem B"},{"key":"1018_CR27","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1111\/j.1747-0285.2008.00707.x","volume":"72","author":"AM J\u00f8rgensen","year":"2008","unstructured":"J\u00f8rgensen AM, Topiol S (2008) Driving forces for ligand migration in the leucine transporter. Chem Biol Drug Des 72:265\u2013272","journal-title":"Chem Biol Drug Des"},{"key":"1018_CR28","doi-asserted-by":"publisher","first-page":"712","DOI":"10.1016\/j.jmgm.2008.11.004","volume":"27","author":"A Lauria","year":"2009","unstructured":"Lauria A, Ippolito M, Almerico AM (2009) Inside the Hsp90 inhibitors binding mode through induced fit docking. J Mol Graph Model 27:712\u2013722","journal-title":"J Mol Graph Model"},{"key":"1018_CR29","doi-asserted-by":"publisher","first-page":"512","DOI":"10.1016\/j.jmgm.2008.09.002","volume":"27","author":"H Wang","year":"2008","unstructured":"Wang H, Aslanian R, Madison VS (2008) Induced-fit docking of mometasone furoate and further evidence for glucocorticoid receptor 17[alpha] pocket flexibility. J Mol Graph\u00a027:512\u2013521","journal-title":"J Mol Graph"},{"key":"1018_CR30","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1021\/jm0306430","volume":"47","author":"RA Friesner","year":"2004","unstructured":"Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739\u20131749","journal-title":"J Med Chem"},{"key":"1018_CR31","doi-asserted-by":"crossref","first-page":"2356","DOI":"10.1021\/ci900212v","volume":"49","author":"NK Salam","year":"2009","unstructured":"Salam NK, Nuti R, Sherman W (2009) Novel method for generating structure-based pharmacophores using energetic analysis. J Chem Inf Model 49:2356\u20132368","journal-title":"J Chem Inf Model"},{"key":"1018_CR32","doi-asserted-by":"crossref","first-page":"6507","DOI":"10.1021\/jm070593p","volume":"50","author":"SB Nabuurs","year":"2007","unstructured":"Nabuurs SB, Wagener M, de Vlieg J (2007) A flexible approach to induced fit docking. J Med Chem 50:6507\u20136518","journal-title":"J Med Chem"},{"key":"1018_CR33","doi-asserted-by":"crossref","first-page":"2878","DOI":"10.1021\/ja993663t","volume":"122","author":"EM Duffy","year":"2000","unstructured":"Duffy EM, Jorgensen WL (2000) Prediction of properties from simulations: free energies of solvation in hexadecane, octanol, and water. J Am Chem 122:2878\u20132888","journal-title":"J Am Chem"},{"key":"1018_CR34","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/S0169-409X(96)00423-1","volume":"23","author":"CA Lipinski","year":"1997","unstructured":"Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (1997) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 23:3\u201325","journal-title":"Adv Drug Deliv Rev"}],"container-title":["Journal of Molecular Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-011-1018-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00894-011-1018-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-011-1018-3","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-011-1018-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,29]],"date-time":"2022-07-29T17:03:26Z","timestamp":1659114206000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00894-011-1018-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,3,29]]},"references-count":34,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,1]]}},"alternative-id":["1018"],"URL":"https:\/\/doi.org\/10.1007\/s00894-011-1018-3","relation":{},"ISSN":["1610-2940","0948-5023"],"issn-type":[{"value":"1610-2940","type":"print"},{"value":"0948-5023","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,3,29]]},"assertion":[{"value":"3 November 2010","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 February 2011","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 March 2011","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}]}}