{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T14:45:08Z","timestamp":1761489908779},"reference-count":43,"publisher":"Springer Science and Business Media LLC","issue":"4","license":[{"start":{"date-parts":[[2016,3,11]],"date-time":"2016-03-11T00:00:00Z","timestamp":1457654400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Mol Model"],"published-print":{"date-parts":[[2016,4]]},"DOI":"10.1007\/s00894-016-2945-9","type":"journal-article","created":{"date-parts":[[2016,3,11]],"date-time":"2016-03-11T05:09:29Z","timestamp":1457672969000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Modeling of babesipain-1 and identification of natural and synthetic leads for bovine babesiosis drug development"],"prefix":"10.1007","volume":"22","author":[{"given":"Potshangbam Angamba","family":"Meetei","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"R. S.","family":"Rathore","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"N. Prakash","family":"Prabhu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vaibhav","family":"Vindal","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,3,11]]},"reference":[{"key":"2945_CR1","doi-asserted-by":"crossref","first-page":"1788","DOI":"10.1016\/j.meegid.2012.07.004","volume":"12","author":"L Schnittger","year":"2012","unstructured":"Schnittger L, Rodriguez AE, Florin-Christensen M, Morrison DA (2012) Babesia: a world emerging. Infect Genet Evol 12:1788\u20131809. doi: 10.1016\/j.meegid.2012.07.004","journal-title":"Infect Genet Evol"},{"issue":"Suppl","key":"2945_CR2","doi-asserted-by":"crossref","first-page":"S247","DOI":"10.1017\/S0031182004005190","volume":"129","author":"R Bock","year":"2004","unstructured":"Bock R, Jackson L, de Vos A, Jorgensen W (2004) Babesiosis of cattle. Parasitology 129(Suppl):S247\u2013269","journal-title":"Parasitology"},{"key":"2945_CR3","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.vetpar.2011.05.032","volume":"180","author":"CE Suarez","year":"2011","unstructured":"Suarez CE, Noh S (2011) Emerging perspectives in the research of bovine babesiosis and anaplasmosis. Vet Parasitol 180:109\u2013125. doi: 10.1016\/j.vetpar.2011.05.032","journal-title":"Vet Parasitol"},{"key":"2945_CR4","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/j.vetpar.2006.01.042","volume":"138","author":"DT Waal de","year":"2006","unstructured":"de Waal DT, Combrink MP (2006) Live vaccines against bovine babesiosis. Vet Parasitol 138:88\u201396. doi: 10.1016\/j.vetpar.2006.01.042","journal-title":"Vet Parasitol"},{"key":"2945_CR5","doi-asserted-by":"crossref","first-page":"G29","DOI":"10.1016\/j.vaccine.2008.09.070","volume":"26","author":"L Fish","year":"2008","unstructured":"Fish L, Leibovich B, Krigel Y et al (2008) Vaccination of cattle against B. bovis infection with live attenuated parasites and non-viable immunogens. Vaccine 26:G29\u2013G33. doi: 10.1016\/j.vaccine.2008.09.070","journal-title":"Vaccine"},{"key":"2945_CR6","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/j.vetpar.2006.01.048","volume":"138","author":"HJ Vial","year":"2006","unstructured":"Vial HJ, Gorenflot A (2006) Chemotherapy against babesiosis. Vet Parasitol 138:147\u2013160. doi: 10.1016\/j.vetpar.2006.01.048","journal-title":"Vet Parasitol"},{"key":"2945_CR7","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1016\/j.parint.2010.02.006","volume":"59","author":"M AbouLaila","year":"2010","unstructured":"AbouLaila M, Sivakumar T, Yokoyama N, Igarashi I (2010) Inhibitory effect of terpene nerolidol on the growth of Babesia parasites. Parasitol Int 59:278\u2013282. doi: 10.1016\/j.parint.2010.02.006","journal-title":"Parasitol Int"},{"key":"2945_CR8","doi-asserted-by":"crossref","first-page":"334","DOI":"10.4269\/ajtmh.2003.68.334","volume":"68","author":"S Bork","year":"2003","unstructured":"Bork S, Yokoyama N, Matsuo T et al (2003) Growth inhibitory effect of triclosan on equine and bovine Babesia parasites. Am J Trop Med Hyg 68:334\u2013340","journal-title":"Am J Trop Med Hyg"},{"key":"2945_CR9","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1007\/BF02356129","volume":"17","author":"I Yeruham","year":"1985","unstructured":"Yeruham I, Pipano E, Davidson M (1985) A field strain of Babesia bovis apparently resistant to amicarbalide isethionate. Trop Anim Health Prod 17:29\u201330","journal-title":"Trop Anim Health Prod"},{"key":"2945_CR10","doi-asserted-by":"crossref","first-page":"1401","DOI":"10.1371\/journal.ppat.0030148","volume":"3","author":"KA Brayton","year":"2007","unstructured":"Brayton KA, Lau AOT, Herndon DR et al (2007) Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoa. PLoS Pathog 3:1401\u20131413. doi: 10.1371\/journal.ppat.0030148","journal-title":"PLoS Pathog"},{"key":"2945_CR11","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1111\/j.1865-1682.2010.01102.x","volume":"57","author":"TM Martins","year":"2010","unstructured":"Martins TM, Gon\u00e7alves LMD, Capela R et al (2010) Effect of synthesized inhibitors on babesipain-1, a new cysteine protease from the bovine piroplasm Babesia bigemina: effect of synthesized inhibitors on babesipain-1. Transbound Emerg Dis 57:68\u201369. doi: 10.1111\/j.1865-1682.2010.01102.x","journal-title":"Transbound Emerg Dis"},{"key":"2945_CR12","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.exppara.2007.04.009","volume":"117","author":"K Okubo","year":"2007","unstructured":"Okubo K, Yokoyama N, Govind Y et al (2007) Babesia bovis: effects of cysteine protease inhibitors on in vitro growth. Exp Parasitol 117:214\u2013217. doi: 10.1016\/j.exppara.2007.04.009","journal-title":"Exp Parasitol"},{"key":"2945_CR13","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1016\/j.exppara.2010.07.012","volume":"127","author":"TM Martins","year":"2011","unstructured":"Martins TM, do Ros\u00e1rio VE, Domingos A (2011) Identification of papain-like cysteine proteases from the bovine piroplasm Babesia bigemina and evolutionary relationship of piroplasms C1 family of cysteine proteases. Exp Parasitol 127:184\u2013194. doi: 10.1016\/j.exppara.2010.07.012","journal-title":"Exp Parasitol"},{"key":"2945_CR14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.actatropica.2011.09.008","volume":"121","author":"TM Martins","year":"2012","unstructured":"Martins TM, do Ros\u00e1rio VE, Domingos A (2012) Expression and characterization of the Babesia bigemina cysteine protease BbiCPL1. Acta Trop 121:1\u20135. doi: 10.1016\/j.actatropica.2011.09.008","journal-title":"Acta Trop"},{"key":"2945_CR15","doi-asserted-by":"crossref","first-page":"3063","DOI":"10.1073\/pnas.90.7.3063","volume":"90","author":"KM Karrer","year":"1993","unstructured":"Karrer KM, Peiffer SL, DiTomas ME (1993) Two distinct gene subfamilies within the family of cysteine protease genes. Proc Natl Acad Sci USA 90:3063\u20133067","journal-title":"Proc Natl Acad Sci USA"},{"key":"2945_CR16","doi-asserted-by":"crossref","first-page":"2965","DOI":"10.1046\/j.1432-1033.2000.01312.x","volume":"267","author":"S Kreusch","year":"2000","unstructured":"Kreusch S, Fehn M, Maubach G et al (2000) An evolutionarily conserved tripartite tryptophan motif stabilizes the prodomains of cathepsin L-like cysteine proteases. Eur J Biochem FEBS 267:2965\u20132972","journal-title":"Eur J Biochem FEBS"},{"key":"2945_CR17","doi-asserted-by":"crossref","first-page":"10838","DOI":"10.1074\/jbc.270.28.16645","volume":"270","author":"T Vernet","year":"1995","unstructured":"Vernet T, Berti PJ, de Montigny C et al (1995) Processing of the papain precursor. The ionization state of a conserved amino acid motif within the Pro region participates in the regulation of intramolecular processing. J Biol Chem 270:10838\u201310846","journal-title":"J Biol Chem"},{"key":"2945_CR18","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1038\/218929a0","volume":"218","author":"J Drenth","year":"1968","unstructured":"Drenth J, Jansonius JN, Koekoek R et al (1968) Structure of Papain. Nature 218:929\u2013932. doi: 10.1038\/218929a0","journal-title":"Nature"},{"key":"2945_CR19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18388\/abp.2001_5108","volume":"48","author":"Z Grzonka","year":"2001","unstructured":"Grzonka Z, Jankowska E, Kasprzykowski F et al (2001) Structural studies of cysteine proteases and their inhibitors. Acta Biochim Pol 48:1\u201320","journal-title":"Acta Biochim Pol"},{"key":"2945_CR20","doi-asserted-by":"crossref","first-page":"D154","DOI":"10.1093\/nar\/gki070","volume":"33","author":"A Bairoch","year":"2005","unstructured":"Bairoch A, Apweiler R, Wu CH et al (2005) The universal protein resource (UniProt). Nucleic Acids Res 33:D154\u2013D159. doi: 10.1093\/nar\/gki070","journal-title":"Nucleic Acids Res"},{"key":"2945_CR21","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 et al (2000) The protein data bank. Nucleic Acids Res 28:235\u2013242. doi: 10.1093\/nar\/28.1.235","journal-title":"Nucleic Acids Res"},{"key":"2945_CR22","unstructured":"Schr\u00f6dinger LLC (2014) Prime, version3.4. Schr\u00f6dinger, LLC, New York"},{"key":"2945_CR23","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. doi: 10.1021\/ja9621760","journal-title":"J Am Chem Soc"},{"key":"2945_CR24","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1002\/jcc.10045","volume":"23","author":"E Gallicchio","year":"2002","unstructured":"Gallicchio E, Zhang LY, Levy RM (2002) The SGB\/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators. J Comput Chem 23:517\u2013529. doi: 10.1002\/jcc.10045","journal-title":"J Comput Chem"},{"key":"2945_CR25","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1002\/prot.10613","volume":"55","author":"MP Jacobson","year":"2004","unstructured":"Jacobson MP, Pincus DL, Rapp CS et al (2004) A hierarchical approach to all-atom protein loop prediction. Proteins Struct Funct Bioinf 55:351\u2013367. doi: 10.1002\/prot.10613","journal-title":"Proteins Struct Funct Bioinf"},{"key":"2945_CR26","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 stereochemical quality of protein structures. J Appl Crystallogr 26:283\u2013291","journal-title":"J Appl Crystallogr"},{"key":"2945_CR27","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/1472-6807-9-35","volume":"9","author":"P Benkert","year":"2009","unstructured":"Benkert P, Schwede T, Tosatto SC (2009) QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information. BMC Struct Biol 9:35. doi: 10.1186\/1472-6807-9-35","journal-title":"BMC Struct Biol"},{"key":"2945_CR28","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1093\/bioinformatics\/btq662","volume":"27","author":"P Benkert","year":"2011","unstructured":"Benkert P, Biasini M, Schwede T (2011) Toward the estimation of the absolute quality of individual protein structure models. Bioinf Oxf Engl 27:343\u2013350. doi: 10.1093\/bioinformatics\/btq662","journal-title":"Bioinf Oxf Engl"},{"key":"2945_CR29","volume-title":"Protein preparation wizard","author":"Schr\u00f6dinger LLC","year":"2014","unstructured":"Schr\u00f6dinger LLC (2014) Protein preparation wizard. Schr\u00f6dinger, LLC, New York"},{"key":"2945_CR30","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. doi: 10.1021\/jp003919d","journal-title":"J Phys Chem B"},{"key":"2945_CR31","doi-asserted-by":"crossref","first-page":"1752","DOI":"10.1002\/jcc.20292","volume":"26","author":"JL Banks","year":"2005","unstructured":"Banks JL, Beard HS, Cao Y et al (2005) Integrated modeling program, applied chemical theory (IMPACT). J Comput Chem 26:1752\u20131780. doi: 10.1002\/jcc.20292","journal-title":"J Comput Chem"},{"key":"2945_CR32","doi-asserted-by":"crossref","first-page":"1757","DOI":"10.1021\/ci3001277","volume":"52","author":"JJ Irwin","year":"2012","unstructured":"Irwin JJ, Sterling T, Mysinger MM et al (2012) ZINC: a free tool to discover chemistry for biology. J Chem Inf Model 52:1757\u20131768. doi: 10.1021\/ci3001277","journal-title":"J Chem Inf Model"},{"key":"2945_CR33","unstructured":"Schr\u00f6dinger LLC (2014) LigPrep, version 2.9, Schr\u00f6dinger, LLC, New York"},{"key":"2945_CR34","unstructured":"Schr\u00f6dinger LLC (2014) Glide, version 6.2, Schr\u00f6dinger, LLC, New York"},{"key":"2945_CR35","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 et al (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739\u20131749. doi: 10.1021\/jm0306430","journal-title":"J Med Chem"},{"key":"2945_CR36","doi-asserted-by":"crossref","first-page":"6177","DOI":"10.1021\/jm051256o","volume":"49","author":"RA Friesner","year":"2006","unstructured":"Friesner RA, Murphy RB, Repasky MP et al (2006) Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem 49:6177\u20136196. doi: 10.1021\/jm051256o","journal-title":"J Med Chem"},{"key":"2945_CR37","doi-asserted-by":"crossref","unstructured":"Bowers KJ, Chow E, Xu H et al (2006) Scalable algorithms for molecular dynamics simulations on commodity clusters. In: SC 2006 Conf. Proc. ACMIEEE. IEEE, pp\u00a043\u201343","DOI":"10.1109\/SC.2006.54"},{"key":"2945_CR38","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1063\/1.470117","volume":"103","author":"U Essmann","year":"1995","unstructured":"Essmann U, Perera L, Berkowitz ML et al (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577\u20138593","journal-title":"J Chem Phys"},{"key":"2945_CR39","unstructured":"Schr\u00f6dinger LLC (2014) QikProp, version 3.2, Schr\u00f6dinger, LLC, New York"},{"key":"2945_CR40","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1002\/qsar.200730051","volume":"27","author":"L Ioakimidis","year":"2008","unstructured":"Ioakimidis L, Thoukydidis L, Mirza A et al (2008) Benchmarking the reliability of QikProp. Correlation between experimental and predicted values. QSAR Comb Sci 27:445\u2013456. doi: 10.1002\/qsar.200730051","journal-title":"QSAR Comb Sci"},{"key":"2945_CR41","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1093\/bioinformatics\/16.4.404","volume":"16","author":"LJ McGuffin","year":"2000","unstructured":"McGuffin LJ, Bryson K, Jones DT (2000) The PSIPRED protein structure prediction server. Bioinf Oxf Engl 16:404\u2013405","journal-title":"Bioinf Oxf Engl"},{"key":"2945_CR42","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1002\/pro.2007","volume":"21","author":"A Bagaria","year":"2012","unstructured":"Bagaria A, Jaravine V, Huang YJ et al (2012) Protein structure validation by generalized linear model root-mean-square deviation prediction. Protein Sci Publ Protein Soc 21:229\u2013238. doi: 10.1002\/pro.2007","journal-title":"Protein Sci Publ Protein Soc"},{"key":"2945_CR43","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1002\/prot.20264","volume":"57","author":"Y Zhang","year":"2004","unstructured":"Zhang Y, Skolnick J (2004) Scoring function for automated assessment of protein structure template quality. Proteins 57:702\u2013710. doi: 10.1002\/prot.20264","journal-title":"Proteins"}],"container-title":["Journal of Molecular Modeling"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-016-2945-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s00894-016-2945-9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-016-2945-9","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,9,17]],"date-time":"2020-09-17T00:49:13Z","timestamp":1600303753000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s00894-016-2945-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,3,11]]},"references-count":43,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2016,4]]}},"alternative-id":["2945"],"URL":"https:\/\/doi.org\/10.1007\/s00894-016-2945-9","relation":{},"ISSN":["1610-2940","0948-5023"],"issn-type":[{"value":"1610-2940","type":"print"},{"value":"0948-5023","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,3,11]]},"article-number":"71"}}