{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T11:38:54Z","timestamp":1778758734494,"version":"3.51.4"},"reference-count":58,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2011,7,27]],"date-time":"2011-07-27T00:00:00Z","timestamp":1311724800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0021812","type":"journal-article","created":{"date-parts":[[2011,7,27]],"date-time":"2011-07-27T20:53:01Z","timestamp":1311799981000},"page":"e21812","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":38,"title":["Computational Reverse-Engineering of a Spider-Venom Derived Peptide Active Against Plasmodium falciparum SUB1"],"prefix":"10.1371","volume":"6","author":[{"given":"Giacomo","family":"Bastianelli","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anthony","family":"Bouillon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christophe","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elodie","family":"Crublet","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"St\u00e9phane","family":"P\u00eatres","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olivier","family":"Gorgette","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dung","family":"Le-Nguyen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Christophe","family":"Barale","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Nilges","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2011,7,27]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1038\/nature07361","article-title":"Malaria research in the post-genomic era.","volume":"455","author":"EA Winzeler","year":"2008","journal-title":"Nature"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"4688","DOI":"10.1111\/j.1742-4658.2007.05999.x","article-title":"Drug-resistant malaria - an insight.","volume":"274","author":"JE Hyde","year":"2007","journal-title":"FEBS J"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.2174\/0929867033457494","article-title":"Perspective in antimalarial chemotherapy.","volume":"10","author":"A Kumar","year":"2003","journal-title":"Curr Med Chem"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1016\/j.cell.2007.10.049","article-title":"Subcellular discharge of a serine protease mediates release of invasive malaria parasites from host erythrocytes.","volume":"131","author":"S Yeoh","year":"2007","journal-title":"Cell"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/emboj.2009.22","article-title":"A multifunctional serine protease primes the malaria parasite for red blood cell invasion.","volume":"28","author":"K Koussis","year":"2009","journal-title":"EMBO J"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1097\/QCO.0b013e3282f1673a","article-title":"Strategies to reverse drug resistance in malaria.","volume":"20","author":"TJ Egan","year":"2007","journal-title":"Curr Opin Infect Dis"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"9915","DOI":"10.1021\/bi034376b","article-title":"Structures of phage-display peptides that bind to the malarial surface protein, apical membrane antigen 1, and block erythrocyte invasion.","volume":"42","author":"DW Keizer","year":"2003","journal-title":"Biochemistry"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1021\/jm020104f","article-title":"Synthesis and in vitro studies of novel pyrimidinyl peptidomimetics as potential antimalarial therapeutic agents.","volume":"45","author":"S Zhu","year":"2002","journal-title":"J Med Chem"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1128\/AAC.46.4.1059-1066.2002","article-title":"textitIn vitro antiplasmodium effects of dermaseptin s4 derivatives.","volume":"46","author":"A Dagan","year":"2002","journal-title":"Antimicrob Agents Chemother"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"31609","DOI":"10.1074\/jbc.272.50.31609","article-title":"Selective cytotoxicity of dermaseptin s3 toward intraerythrocytic <italic>Plasmodium falciparum<\/italic> and the underlying molecular basis.","volume":"272","author":"J Ghosh","year":"1997","journal-title":"J Biol Chem"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.febslet.2004.07.019","article-title":"Isolation and characterization of psalmopeotoxin i and ii: two novel antimalarial peptides from the venom of the tarantula <italic>Psalmopoeus cambridgei<\/italic>.","volume":"572","author":"S Choi","year":"2004","journal-title":"FEBS Lett"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"628","DOI":"10.1110\/ps.051860606","article-title":"Solution structure of pcfk1, a spider peptide active against <italic>Plasmodium falciparum<\/italic>.","volume":"15","author":"C Pimentel","year":"2006","journal-title":"Protein Sci"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1016\/j.copbio.2007.04.009","article-title":"Progress in computational protein design.","volume":"18","author":"SM Lippow","year":"2007","journal-title":"Curr Opin Biotechnol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"2427","DOI":"10.1007\/s00018-003-3120-x","article-title":"Canonical protein inhibitors of serine proteases.","volume":"60","author":"D Krowarsch","year":"2003","journal-title":"Cell Mol Life Sci"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"29698","DOI":"10.1074\/jbc.M203088200","article-title":"Expression of recombinant plasmodium falciparum subtilisin-like protease-1 in insect cells. characterization, comparison with the parasite protease, and homology modeling.","volume":"277","author":"C Withers-Martinez","year":"2002","journal-title":"J Biol Chem"},{"key":"ref16","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":"A Sali","year":"1993","journal-title":"J Mol Biol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"1303","DOI":"10.1038\/sj.emboj.7600611","article-title":"The many faces of protease-protein inhibitor interaction.","volume":"24","author":"J Otlewski","year":"2005","journal-title":"EMBO J"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1016\/S0022-2836(03)00610-7","article-title":"Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the ras-raf and ras-ralgds complexes.","volume":"330","author":"H Gohlke","year":"2003","journal-title":"J Mol Biol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1002\/prot.20192","article-title":"Effciency of a second-generation hiv-1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations.","volume":"57","author":"M Leps\u00edk","year":"2004","journal-title":"Proteins"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1002\/prot.20275","article-title":"Computational studies and peptidomimetic design for the human p53-mdm2 complex.","volume":"58","author":"H Zhong","year":"2005","journal-title":"Proteins"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1405","DOI":"10.1016\/j.jmb.2007.06.003","article-title":"Affinity and specificity of protein u1a-rna complex formation based on an additive component free energy model.","volume":"371","author":"BL Kormos","year":"2007","journal-title":"J Mol Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"28572","DOI":"10.1074\/jbc.M303827200","article-title":"Functional characterization of the propeptide of <italic>Plasmodium falciparum<\/italic> subtilisin-like protease-1.","volume":"278","author":"L Jean","year":"2003","journal-title":"J Biol Chem"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/S0041-0101(00)00160-4","article-title":"The cystine knot motif in toxins and implications for drug design.","volume":"39","author":"DJ Craik","year":"2001","journal-title":"Toxicon"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1038\/nchembio.251","article-title":"Computer-aided design of functional protein interactions.","volume":"5","author":"DJ Mandell","year":"2009","journal-title":"Nat Chem Biol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1016\/j.sbi.2009.07.005","article-title":"Computational design of affinity and specificity at protein-protein interfaces.","volume":"19","author":"J Karanicolas","year":"2009","journal-title":"Curr Opin Struct Biol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1016\/j.sbi.2009.02.008","article-title":"Convergence and combination of methods in protein-protein docking.","volume":"19","author":"S Vajda","year":"2009","journal-title":"Curr Opin Struct Biol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1569","DOI":"10.1002\/jcc.21450","article-title":"Basic ingredients of free energy calculations: a review.","volume":"31","author":"CD Christ","year":"2010","journal-title":"J Comput Chem"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"D169","DOI":"10.1093\/nar\/gkn664","article-title":"The universal protein resource (uniprot) 2009.","volume":"37","author":"U Consortium","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank.","volume":"28","author":"HM Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"W604","DOI":"10.1093\/nar\/gkl092","article-title":"Expresso: automatic incorporation of structural information in multiple sequence alignments using 3d-coffee.","volume":"34","author":"F Armougom","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1002\/prot.340120407","article-title":"Stereochemical quality of protein structure coordinates.","volume":"12","author":"AL Morris","year":"1992","journal-title":"Proteins"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/0263-7855(90)80070-V","article-title":"What if: a molecular modeling and drug design program.","volume":"8","author":"G Vriend","year":"1990","journal-title":"J Mol Graph"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/381272a0","article-title":"Errors in protein structures.","volume":"381","author":"RW Hooft","year":"1996","journal-title":"Nature"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.1002\/pro.5560020916","article-title":"Verification of protein structures: patterns of nonbonded atomic interactions.","volume":"2","author":"C Colovos","year":"1993","journal-title":"Protein Sci"},{"key":"ref35","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":"JU Bowie","year":"1991","journal-title":"Science"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1006\/jmbi.1996.0628","article-title":"Deviations from standard atomic volumes as a quality measure for protein crystal structures.","volume":"264","author":"J Pontius","year":"1996","journal-title":"J Mol Biol"},{"key":"ref37","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":"M Wiederstein","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref38","author":"D Case","year":"2006"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1002\/bip.360221211","article-title":"Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.","volume":"22","author":"W Kabsch","year":"1983","journal-title":"Biopolymers"},{"key":"ref40","author":"W DeLano","year":"2002"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1002\/prot.10389","article-title":"Zdock: an initial-stage protein-docking algorithm.","volume":"52","author":"R Chen","year":"2003","journal-title":"Proteins"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1002\/prot.21123","article-title":"Comparison of multiple amber force fields and development of improved protein backbone parameters.","volume":"65","author":"V Hornak","year":"2006","journal-title":"Proteins"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison of simple potential functions for simulating liquid water.","volume":"79","author":"WL Jorgensen","year":"1983","journal-title":"J Chem Phys"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/0021-9991(77)90098-5","article-title":"Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes.","volume":"23","author":"J Ryckaert","year":"1977","journal-title":"J Comput Phys"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle mesh ewald-an nlog(n) method for ewald sums in large systems.","volume":"98","author":"T Darden","year":"1993","journal-title":"J Chem Phys"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1002\/1097-0282(2000)56:4<275::AID-BIP10024>3.0.CO;2-E","article-title":"Theory and applications of the generalized born solvation model in macro-molecular simulations.","volume":"56","author":"V Tsui","year":"2000","journal-title":"Biopolymers"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/0003-9861(59)90090-6","article-title":"Tissue sulfhydryl groups.","volume":"82","author":"GL Ellman","year":"1959","journal-title":"Arch Biochem Biophys"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1126\/science.781840","article-title":"Human malaria parasites in continuous culture.","volume":"193","author":"W Trager","year":"1976","journal-title":"Science"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"710","DOI":"10.1128\/AAC.16.6.710","article-title":"Quantitative assessment of antimalarial activity <italic>in vitro<\/italic> by a semiautomated microdilution technique.","volume":"16","author":"RE Desjardins","year":"1979","journal-title":"Antimicrob Agents Chemother"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1084\/jem.20082826","article-title":"Drug inhibition of hdac3 and epigenetic control of differentiation in apicomplexa parasites.","volume":"206","author":"A Bougdour","year":"2009","journal-title":"J Exp Med"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1073\/pnas.98.1.271","article-title":"Malaria parasite exit from the host erythrocyte: a two-step process requiring extraerythrocytic proteolysis.","volume":"98","author":"BL Salmon","year":"2001","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1002\/cyto.a.20380","article-title":"Development and validation of ow cytometric measurement for parasitemia in cultures of <italic>P. falciparum<\/italic> vitally stained with yoyo-1.","volume":"71","author":"Q Li","year":"2007","journal-title":"Cytometry A"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1002\/prot.1168","article-title":"Enhancement of protein modeling by human intervention in applying the automatic programs 3d-jigsaw and 3d-pssm.","volume":"Suppl 5","author":"PA Bates","year":"2001","journal-title":"Proteins"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"1682","DOI":"10.1093\/bioinformatics\/btg211","article-title":"Consensus alignment for reliable framework prediction in homology modeling.","volume":"19","author":"JC Prasad","year":"2003","journal-title":"Bioinformatics"},{"key":"ref55","first-page":"102","article-title":"Cphmodels 2.0: X3m a computer program to extract 3d models.","author":"O Lund","year":"2002","journal-title":"Abstract at the CASP5 conference A"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"1250","DOI":"10.1093\/bioinformatics\/18.9.1250","article-title":"Esypred3d: Prediction of proteins 3d structures.","volume":"18","author":"C Lambert","year":"2002","journal-title":"Bioinformatics"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"3381","DOI":"10.1093\/nar\/gkg520","article-title":"Swiss-model: An automated protein homology-modeling server.","volume":"31","author":"T Schwede","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/nprot.2009.2","article-title":"Protein structure prediction on the web: a case study using the phyre server.","volume":"4","author":"LA Kelley","year":"2009","journal-title":"Nat Protoc"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0021812","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,9]],"date-time":"2024-04-09T09:16:17Z","timestamp":1712654177000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0021812"}},"subtitle":[],"editor":[{"given":"Annalisa","family":"Pastore","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2011,7,27]]},"references-count":58,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2011,7,27]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0021812","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,7,27]]}}}