{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T14:33:49Z","timestamp":1761489229537},"reference-count":40,"publisher":"Springer Science and Business Media LLC","issue":"9","license":[{"start":{"date-parts":[[2013,9,1]],"date-time":"2013-09-01T00:00:00Z","timestamp":1377993600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2013,9]]},"DOI":"10.1007\/s10822-013-9682-2","type":"journal-article","created":{"date-parts":[[2013,10,15]],"date-time":"2013-10-15T09:36:23Z","timestamp":1381829783000},"page":"823-835","source":"Crossref","is-referenced-by-count":10,"title":["Toward the discovery of inhibitors of babesipain-1, a Babesia bigemina cysteine protease: in vitro evaluation, homology modeling and molecular docking studies"],"prefix":"10.1007","volume":"27","author":[{"given":"Bianca","family":"P\u00e9rez","sequence":"first","affiliation":[]},{"given":"Sandra","family":"Antunes","sequence":"additional","affiliation":[]},{"given":"L\u00eddia M.","family":"Gon\u00e7alves","sequence":"additional","affiliation":[]},{"given":"Ana","family":"Domingos","sequence":"additional","affiliation":[]},{"given":"Jos\u00e9 R. B.","family":"Gomes","sequence":"additional","affiliation":[]},{"given":"Paula","family":"Gomes","sequence":"additional","affiliation":[]},{"given":"C\u00e1tia","family":"Teixeira","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,10,16]]},"reference":[{"issue":"8","key":"9682_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(8):1788","journal-title":"Infect Genet Evol"},{"issue":"10","key":"9682_CR2","doi-asserted-by":"crossref","first-page":"1504","DOI":"10.2174\/092986712799828355","volume":"19","author":"J Mosqueda","year":"2012","unstructured":"Mosqueda J, Olvera-Ramirez A, Aguilar-Tipacamu G, Canto GJ (2012) Current advances in detection and treatment of babesiosis. Curr Med Chem 19(10):1504","journal-title":"Curr Med Chem"},{"issue":"1\u20132","key":"9682_CR3","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(1\u20132):88","journal-title":"Vet Parasitol"},{"issue":"Suppl 6","key":"9682_CR4","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, McElwain T, Shkap V (2008) Vaccination of cattle against B. bovis infection with live attenuated parasites and non-viable immunogens. Vaccine 26(Suppl 6):G29","journal-title":"Vaccine"},{"issue":"1\u20132","key":"9682_CR5","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(1\u20132):147","journal-title":"Vet Parasitol"},{"issue":"1","key":"9682_CR6","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 Rosario VE, Domingos A (2012) Expression and characterization of the Babesia bigemina cysteine protease BbiCPL1. Acta Trop 121(1):1","journal-title":"Acta Trop"},{"key":"9682_CR7","unstructured":"http:\/\/www.sanger.ac.uk\/resources\/downloads\/protozoa\/babesia-bigemina.html . Accessed 08 May 2013"},{"issue":"2","key":"9682_CR8","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, Alhassan A, Igarashi I (2007) Babesia bovis: effects of cysteine protease inhibitors on in vitro growth. Exp Parasitol 117(2):214","journal-title":"Exp Parasitol"},{"issue":"1","key":"9682_CR9","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 Rosario 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(1):184","journal-title":"Exp Parasitol"},{"issue":"Pt 2","key":"9682_CR10","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1042\/0264-6021:3600481","volume":"360","author":"PS Sijwali","year":"2001","unstructured":"Sijwali PS, Shenai BR, Gut J, Singh A, Rosenthal PJ (2001) Expression and characterization of the Plasmodium falciparum haemoglobinase falcipain-3. Biochem J 360(Pt 2):481","journal-title":"Biochem J"},{"issue":"6","key":"9682_CR11","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1097\/QCO.0b013e328315cca9","volume":"21","author":"JH McKerrow","year":"2008","unstructured":"McKerrow JH, Rosenthal PJ, Swenerton R, Doyle P (2008) Development of protease inhibitors for protozoan infections. Curr Opin Infect Dis 21(6):668","journal-title":"Curr Opin Infect Dis"},{"issue":"10","key":"9682_CR12","doi-asserted-by":"crossref","first-page":"1555","DOI":"10.2174\/092986711795328328","volume":"18","author":"C Teixeira","year":"2011","unstructured":"Teixeira C, Gomes JR, Gomes P (2011) Falcipains, Plasmodium falciparum cysteine proteases as key drug targets against malaria. Curr Med Chem 18(10):1555","journal-title":"Curr Med Chem"},{"issue":"12","key":"9682_CR13","doi-asserted-by":"crossref","first-page":"3229","DOI":"10.1016\/j.bmcl.2009.04.100","volume":"19","author":"R Capela","year":"2009","unstructured":"Capela R, Oliveira R, Goncalves LM, Domingos A, Gut J, Rosenthal PJ, Lopes F, Moreira R (2009) Artemisinin-dipeptidyl vinyl sulfone hybrid molecules: design, synthesis and preliminary SAR for antiplasmodial activity and falcipain-2 inhibition. Bioorg Med Chem Lett 19(12):3229","journal-title":"Bioorg Med Chem Lett"},{"issue":"1\u20132","key":"9682_CR14","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, Goncalves LM, Capela R, Moreira R, do Rosario VE, Domingos A (2010) Effect of synthesized inhibitors on babesipain-1, a new cysteine protease from the bovine piroplasm Babesia bigemina. Transbound Emerg Dis 57(1\u20132):68","journal-title":"Transbound Emerg Dis"},{"key":"9682_CR15","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1016\/j.ejmech.2012.05.022","volume":"54","author":"BC Perez","year":"2012","unstructured":"Perez BC, Teixeira C, Figueiras M, Gut J, Rosenthal PJ, Gomes JR, Gomes P (2012) Novel cinnamic acid\/4-aminoquinoline conjugates bearing non-proteinogenic amino acids: towards the development of potential dual action antimalarials. Eur J Med Chem 54:887","journal-title":"Eur J Med Chem"},{"issue":"Database issue","key":"9682_CR16","first-page":"D71","volume":"40","author":"R Apweiler","year":"2012","unstructured":"Apweiler R, O\u2019onovan C, Magrane M, Alam-Faruque Y, Antunes R, Bely B, Bingley M et al (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40(Database issue):D71","journal-title":"Nucleic Acids Res"},{"issue":"Web Server issu","key":"9682_CR17","doi-asserted-by":"crossref","first-page":"W13","DOI":"10.1093\/nar\/gkr245","volume":"39","author":"P Tommaso Di","year":"2011","unstructured":"Di Tommaso P, Moretti S, Xenarios I, Orobitg M, Montanyola A, Chang JM, Taly JF, Notredame C (2011) T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Res 39(Web Server issue):W13","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"9682_CR18","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1006\/jmbi.1993.1626","volume":"234","author":"A Sali","year":"1993","unstructured":"Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234(3):779","journal-title":"J Mol Biol"},{"issue":"4","key":"9682_CR19","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(4):355","journal-title":"Proteins"},{"issue":"Web Server issu","key":"9682_CR20","doi-asserted-by":"crossref","first-page":"W407","DOI":"10.1093\/nar\/gkm290","volume":"35","author":"M Wiederstein","year":"2007","unstructured":"Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35(Web Server issue):W407","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"9682_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 stereochemical quality of protein structures. J Appl Crystallogr 26(2):283","journal-title":"J Appl Crystallogr"},{"key":"9682_CR22","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","journal-title":"BMC Struct Biol"},{"issue":"5","key":"9682_CR23","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1110\/ps.0236803","volume":"12","author":"B Wallner","year":"2003","unstructured":"Wallner B, Elofsson A (2003) Can correct protein models be identified? Protein Sci 12(5):1073","journal-title":"Protein Sci"},{"issue":"8","key":"9682_CR24","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1007\/s10822-011-9459-4","volume":"25","author":"C Teixeira","year":"2011","unstructured":"Teixeira C, Gomes JR, Couesnon T, Gomes P (2011) Molecular docking and 3D-quantitative structure activity relationship analyses of peptidyl vinyl sulfones: Plasmodium falciparum cysteine proteases inhibitors. J Comput Aided Mol Des 25(8):763","journal-title":"J Comput Aided Mol Des"},{"issue":"Web Server issu","key":"9682_CR25","doi-asserted-by":"crossref","first-page":"W368","DOI":"10.1093\/nar\/gki464","volume":"33","author":"JC Gordon","year":"2005","unstructured":"Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, Onufriev A (2005) H++: a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Res 33(Web Server issue):W368","journal-title":"Nucleic Acids Res"},{"key":"9682_CR26","volume-title":"AMBER 10","author":"DA Case","year":"2008","unstructured":"Case DA, Darden TA, Cheatham TE, Simmerling CLI, Wang J, Duke RE, Luo R, Crowley M, Walker RC, Zhang W, Merz KM, Wang B, Hayik S, Roitberg A, Seabra G, Kolossv\u00e1ry KF, Wong KF, Paesani F, Vanicek F, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Mathews DH, Seetin MG, Sagui C, Babin V, Kollman PA (2008) AMBER 10. University of California, San Francisco"},{"issue":"16","key":"9682_CR27","doi-asserted-by":"crossref","first-page":"1999","DOI":"10.1002\/jcc.10349","volume":"24","author":"Y Duan","year":"2003","unstructured":"Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24(16):1999","journal-title":"J Comput Chem"},{"issue":"3","key":"9682_CR28","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1006\/jmbi.1996.0897","volume":"267","author":"G Jones","year":"1997","unstructured":"Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267(3):727","journal-title":"J Mol Biol"},{"key":"9682_CR29","unstructured":"MarvinSketch 5.12.2 (2013) ChemAxon. http:\/\/www.chemaxon.com"},{"issue":"6","key":"9682_CR30","doi-asserted-by":"crossref","first-page":"1552","DOI":"10.1021\/ja00839a047","volume":"97","author":"M Charton","year":"1975","unstructured":"Charton M (1975) Steric effects. I. Esterification and acid-catalyzed hydrolysis of esters. J Am Chem Soc 97(6):1552","journal-title":"J Am Chem Soc"},{"issue":"Database issue","key":"9682_CR31","doi-asserted-by":"crossref","first-page":"D227","DOI":"10.1093\/nar\/gkp971","volume":"38","author":"ND Rawlings","year":"2010","unstructured":"Rawlings ND, Barrett AJ, Bateman A (2010) MEROPS: the peptidase database. Nucleic Acids Res 38(Database issue):D227","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"9682_CR32","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0166-6851(01)00438-8","volume":"120","author":"M Sajid","year":"2002","unstructured":"Sajid M, McKerrow JH (2002) Cysteine proteases of parasitic organisms. Mol Biochem Parasitol 120(1):1","journal-title":"Mol Biochem Parasitol"},{"issue":"6","key":"9682_CR33","doi-asserted-by":"crossref","first-page":"990","DOI":"10.1110\/ps.073344908","volume":"17","author":"P Larsson","year":"2008","unstructured":"Larsson P, Wallner B, Lindahl E, Elofsson A (2008) Using multiple templates to improve quality of homology models in automated homology modeling. Protein Sci 17(6):990","journal-title":"Protein Sci"},{"issue":"11","key":"9682_CR34","doi-asserted-by":"crossref","first-page":"2507","DOI":"10.1110\/ps.062416606","volume":"15","author":"MY Shen","year":"2006","unstructured":"Shen MY, Sali A (2006) Statistical potential for assessment and prediction of protein structures. Protein Sci 15(11):2507","journal-title":"Protein Sci"},{"issue":"3","key":"9682_CR35","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. Bioinformatics 27(3):343","journal-title":"Bioinformatics"},{"key":"9682_CR36","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/1471-2105-2-5","volume":"2","author":"S Cristobal","year":"2001","unstructured":"Cristobal S, Zemla A, Fischer D, Rychlewski L, Elofsson A (2001) A study of quality measures for protein threading models. BMC Bioinform 2:5","journal-title":"BMC Bioinform"},{"issue":"9","key":"9682_CR37","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1093\/bioinformatics\/16.9.776","volume":"16","author":"N Siew","year":"2000","unstructured":"Siew N, Elofsson A, Rychlewski L, Fischer D (2000) MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics 16(9):776","journal-title":"Bioinformatics"},{"issue":"5145","key":"9682_CR38","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, Swen HM, Wolthers BG (1968) Structure of papain. Nature 218(5145):929","journal-title":"Nature"},{"issue":"8","key":"9682_CR39","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1016\/S0969-2126(00)00173-8","volume":"8","author":"LS Brinen","year":"2000","unstructured":"Brinen LS, Hansell E, Cheng J, Roush WR, McKerrow JH, Fletterick RJ (2000) A target within the target: probing cruzain\u2019s P1\u2032 site to define structural determinants for the Chagas\u2019 disease protease. Structure\u00a08(8):831","journal-title":"Structure"},{"issue":"3","key":"9682_CR40","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1021\/jm8013663","volume":"52","author":"ID Kerr","year":"2009","unstructured":"Kerr ID, Lee JH, Pandey KC, Harrison A, Sajid M, Rosenthal PJ, Brinen LS (2009) Structures of falcipain-2 and falcipain-3 bound to small molecule inhibitors: implications for substrate specificity. J Med Chem 52(3):852","journal-title":"J Med Chem"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-013-9682-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10822-013-9682-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-013-9682-2","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,31]],"date-time":"2019-05-31T01:23:14Z","timestamp":1559265794000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10822-013-9682-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,9]]},"references-count":40,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2013,9]]}},"alternative-id":["9682"],"URL":"https:\/\/doi.org\/10.1007\/s10822-013-9682-2","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"value":"0920-654X","type":"print"},{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,9]]}}}