{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T02:14:36Z","timestamp":1792808076813,"version":"4.5.0"},"reference-count":37,"publisher":"American Chemical Society (ACS)","issue":"27","license":[{"start":{"date-parts":[[2020,6,26]],"date-time":"2020-06-26T00:00:00Z","timestamp":1593129600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/pubs.acs.org\/page\/policy\/authorchoice_termsofuse.html"}],"funder":[{"DOI":"10.13039\/501100006507","name":"Funda\u00c3\u00a7\u00c3\u00a3o Oswaldo Cruz","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006507","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"Minist\u00c3\u00a9rio da Ci\u00c3\u00aancia, Tecnologia e Inova\u00c3\u00a7\u00c3\u00a3o","doi-asserted-by":"publisher","award":["431296\/2018-9"],"award-info":[{"award-number":["431296\/2018-9"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"Minist\u00c3\u00a9rio da Ci\u00c3\u00aancia, Tecnologia e Inova\u00c3\u00a7\u00c3\u00a3o","doi-asserted-by":"publisher","award":["457937\/2014-9"],"award-info":[{"award-number":["457937\/2014-9"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002322","name":"Coordena\u00c3\u00a7\u00c3\u00a3o de Aperfei\u00c3\u00a7oamento de Pessoal de N\u00c3\u00advel Superior","doi-asserted-by":"publisher","award":["88887.360984\/2019-00"],"award-info":[{"award-number":["88887.360984\/2019-00"]}],"id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Funda\u00c3\u00a7\u00c3\u00a3o Cearense de Apoio ao Desenvolvimento Cient\u00c3\u00adfico e Tecnol\u00c3\u00b3gico","award":["BMD-0008-01053.01.12\/19"],"award-info":[{"award-number":["BMD-0008-01053.01.12\/19"]}]},{"name":"Funda\u00c3\u00a7\u00c3\u00a3o Cearense de Apoio ao Desenvolvimento Cient\u00c3\u00adfico e Tecnol\u00c3\u00b3gico","award":["FPB-0157-00005.01.01\/19"],"award-info":[{"award-number":["FPB-0157-00005.01.01\/19"]}]},{"name":"National Institute of Science and Technology on Neuroimmunomodulation - INCT-NIM"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Integrins are cell adhesion receptors that transmit bidirectional signals across the plasma membrane. They are noncovalently linked heterodimeric molecules consisting of two subunits and act as biomarkers in several pathologies. Thus, according to the increase of therapeutic antibody production, some efforts have been applied to produce anti-integrin antibodies. Here, we purposed to evaluate methods of generation and identification of the binding pose of integrin\u2013antibody complexes, through protein\u2013protein docking and molecular dynamics simulations, and propose a strategy to assure the confidence of the final model and avoid false-positive poses. The results show that ClusPro and GRAMM-X were the best programs to generate the native pose of integrin\u2013antibody complexes. Furthermore, we were able to recover and to ensure that the selected pose is the native one by using a simple rule. All complexes from ClusPro in which the first model had the lowest energy, at least 5% more negative than the second one, were correctly predicted. Therefore, our methodology seems to be efficient to avoid misranking of wrong poses for integrin\u2013antibody complexes. In cases where the rule is inconclusive, we proposed the use of heated molecular dynamics to identify the native pose characterized by RMSDi &amp;lt;0.5 nm. We believe that the set of methods presented here helps in the rational design of anti-integrin antibodies, giving some insights on the development of new biopharmaceuticals.<\/jats:p>","DOI":"10.1021\/acsomega.0c00226","type":"journal-article","created":{"date-parts":[[2020,6,27]],"date-time":"2020-06-27T03:48:30Z","timestamp":1593229710000},"page":"16379-16385","source":"Crossref","is-referenced-by-count":8,"title":["Guidelines To Predict Binding Poses of Antibody\u2013Integrin\nComplexes"],"prefix":"10.1021","volume":"5","author":[{"given":"Beatriz","family":"Chaves","sequence":"first","affiliation":[{"name":"Oswaldo Cruz Foundation , , Ceara. Av Sao Jose, S\/N, CEP , , ,","place":["Eusebio, Ceara\u0301, Brazil, 61760-000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5613-7194","authenticated-orcid":true,"given":"Geraldo R.","family":"Sartori","sequence":"additional","affiliation":[{"name":"Oswaldo Cruz Foundation , , Ceara. Av Sao Jose, S\/N, CEP , , ,","place":["Eusebio, Ceara\u0301, Brazil, 61760-000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Disraeli C. A.","family":"Vasconcelos","sequence":"additional","affiliation":[{"name":"Oswaldo Cruz Foundation , , Ceara. Av Sao Jose, S\/N, CEP , , ,","place":["Eusebio, Ceara\u0301, Brazil, 61760-000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wilson","family":"Savino","sequence":"additional","affiliation":[{"name":"Oswaldo Cruz Institute\/Oswaldo Cruz Foundation , , ,","place":["Rio de Janeiro, Brazil, 21040-360"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8353-3034","authenticated-orcid":true,"given":"Ernesto R.","family":"Caffarena","sequence":"additional","affiliation":[{"name":"Oswaldo Cruz Foundation , , ,","place":["Rio de Janeiro, Brazil, 21040-222"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vini\u0301cius","family":"Cotta-de-Almeida","sequence":"additional","affiliation":[{"name":"Oswaldo Cruz Institute\/Oswaldo Cruz Foundation , , ,","place":["Rio de Janeiro, Brazil, 21040-360"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joa\u0303o H. M.","family":"da Silva","sequence":"additional","affiliation":[{"name":"Oswaldo Cruz Foundation , , Ceara. Av Sao Jose, S\/N, CEP , , ,","place":["Eusebio, Ceara\u0301, Brazil, 61760-000"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2020,6,26]]},"reference":[{"key":"2026090323132741900_cit1","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1016\/S0092-8674(02)00971-6","article-title":"Integrins:\nBidirectional, Allosteric Signaling Machines In Their Roles as Major\nAdhesion Receptors","volume":"110","author":"Hynes","year":"2002","journal-title":"Cell"},{"key":"2026090323132741900_cit2","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1002\/jcp.21237","article-title":"Cell-matrix adhesion","volume":"213","author":"Berrier","year":"2007","journal-title":"J. Cell.\nPhysiol."},{"key":"2026090323132741900_cit3","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1186\/gb-2007-8-5-215","article-title":"The Integrins","volume":"8","author":"Takada","year":"2007","journal-title":"Genome Biol."},{"key":"2026090323132741900_cit4","doi-asserted-by":"publisher","first-page":"a004994","DOI":"10.1101\/cshperspect.a004994","article-title":"Integrin\nStructure, Activation, and Interactions","volume":"3","author":"Campbell","year":"2011","journal-title":"Cold\nSpring Harb. Perspect. Biol."},{"key":"2026090323132741900_cit5","doi-asserted-by":"publisher","first-page":"20","DOI":"10.4161\/cam.18702","article-title":"The Regulation of Integrin\nFunction by Divalent Cations","volume":"6","author":"Zhang","year":"2012","journal-title":"Cell Adh. Migr."},{"key":"2026090323132741900_cit6","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/S0079-6336(02)80008-0","article-title":"Collagen-Binding I Domain Integrins\n\u2500 What Do They Do?","volume":"37","author":"Gullberg","year":"2002","journal-title":"Prog. Histochem.\nCytochem."},{"key":"2026090323132741900_cit7","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1038\/s41580-019-0134-2","article-title":"Integrins\nas Biomechanical Sensors\nof the Microenvironment","volume":"20","author":"Kechagia","year":"2019","journal-title":"Nat. Rev. Mol. Cell\nBiol."},{"key":"2026090323132741900_cit8","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1016\/j.pharmthera.2011.12.008","article-title":"Integrins as Receptor\nTargets for Neurological Disorders","volume":"134","author":"Wu","year":"2012","journal-title":"Pharmacol.\nTher."},{"key":"2026090323132741900_cit9","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1038\/nri2763","article-title":"Therapeutic\nAntibodies: Past, Present and Future","volume":"10","author":"Leavy","year":"2010","journal-title":"Nat. Rev.\nImmunol."},{"key":"2026090323132741900_cit10","unstructured":"Reuters Brand Feauture.\n          . Monoclonal Antibody Market 2019-2025\nGrowth, Key Players, Size, Demands and Forecasts\u2500Reuters. https:\/\/www.reuters.com\/brandfeatures\/venture-capital\/article?id=101636 (accessed Sep 5, 2019)."},{"key":"2026090323132741900_cit11","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1038\/nrd.2017.227","article-title":"Next Generation\nAntibody Drugs: Pursuit of the \u201cHigh-Hanging\nFruit","volume":"17","author":"Carter","year":"2018","journal-title":"Nat Rev Drug Discov"},{"key":"2026090323132741900_cit12","volume-title":"Abciximab","author":"Stoffer","year":"2019"},{"key":"2026090323132741900_cit13","doi-asserted-by":"publisher","first-page":"1526","DOI":"10.1002\/cncr.24821","article-title":"A Randomized Phase\n2 Study of Etaracizumab, a Monoclonal Antibody against Integrin \u03b1 v \u03b2 3, \u00b1 Dacarbazine in Patients with\nStage IV Metastatic Melanoma","volume":"116","author":"Hersey","year":"2010","journal-title":"Cancer"},{"key":"2026090323132741900_cit14","unstructured":"Drugs.com. Tysabri (natalizumab) FDA Approval History - Drugs.com. https:\/\/www.drugs.com\/history\/tysabri.html (accessed Dec 29, 2018)."},{"key":"2026090323132741900_cit15","doi-asserted-by":"publisher","first-page":"2457","DOI":"10.3748\/wjg.v24.i23.2457","article-title":"Vedolizumab\nfor Inflammatory Bowel Disease: From Randomized Controlled Trials\nto Real-Life Evidence","volume":"24","author":"Scribano","year":"2018","journal-title":"World J. Gastroenterol."},{"key":"2026090323132741900_cit16","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1016\/J.SBI.2018.04.007","article-title":"Computational Design of Antibodies","volume":"51","author":"Fischman","year":"2018","journal-title":"Curr. Opin.\nStruct. Biol."},{"key":"2026090323132741900_cit17","doi-asserted-by":"publisher","first-page":"2121","DOI":"10.1016\/j.celrep.2018.10.081","article-title":"Computational Design of Epitope-Specific\nFunctional Antibodies","volume":"25","author":"Nimrod","year":"2018","journal-title":"Cell Rep"},{"key":"2026090323132741900_cit18","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1002\/prot.22564","article-title":"Present and Future Challenges and\nLimitations in Protein-Protein Docking","volume":"78","author":"Pons","year":"2010","journal-title":"Proteins"},{"key":"2026090323132741900_cit19","doi-asserted-by":"publisher","first-page":"8145","DOI":"10.1038\/s41598-017-08414-y","article-title":"Structure-Based Cross-Docking Analysis of Antibody\u2013Antigen\nInteractions","volume":"7","author":"Kilambi","year":"2017","journal-title":"Sci. Rep."},{"key":"2026090323132741900_cit20","volume-title":"Molecular Modelling:\nPrinciples and Applications","author":"Leach","year":"2001"},{"key":"2026090323132741900_cit21","doi-asserted-by":"publisher","first-page":"2189","DOI":"10.1021\/acs.jcim.0c00057","article-title":"Improving Protein-Ligand\nDocking Results with High-Throughput Molecular\nDynamics Simulations","volume":"60","author":"Guterres","year":"2020","journal-title":"J. Chem. Inf. Model."},{"key":"2026090323132741900_cit22","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1021\/acs.jcim.7b00588","article-title":"Applying Pose Clustering\nand MD Simulations\nto Eliminate False Positives in Molecular Docking","volume":"58","author":"Makeneni","year":"2018","journal-title":"J. Chem. Inf. Model."},{"key":"2026090323132741900_cit23","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006182","article-title":"Assessment of Ab Initio Models of\nProtein Complexes by Molecular Dynamics","volume":"14","author":"Radom","year":"2018","journal-title":"PLoS\nComput. Biol."},{"key":"2026090323132741900_cit24","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic\nAcids Res."},{"key":"2026090323132741900_cit25","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1038\/nprot.2016.169","article-title":"The ClusPro Web Server\nfor Protein-Protein Docking","volume":"12","author":"Kozakov","year":"2017","journal-title":"Nat. Protoc."},{"key":"2026090323132741900_cit26","doi-asserted-by":"publisher","first-page":"2608","DOI":"10.1093\/bioinformatics\/bts493","article-title":"Application\nof asymmetric statistical potentials to antibody-protein docking","volume":"28","author":"Brenke","year":"2012","journal-title":"Bioinformatics"},{"key":"2026090323132741900_cit27","doi-asserted-by":"publisher","first-page":"W363","DOI":"10.1093\/nar\/gki481","article-title":"PatchDock and SymmDock:\nServers for Rigid and Symmetric Docking","volume":"33","author":"Schneidman-Duhovny","year":"2005","journal-title":"Nucleic\nAcids Res."},{"key":"2026090323132741900_cit28","doi-asserted-by":"publisher","first-page":"1771","DOI":"10.1093\/bioinformatics\/btu097","article-title":"ZDOCK Server: Interactive\nDocking Prediction of Protein-Protein Complexes\nand Symmetric Multimers","volume":"30","author":"Pierce","year":"2014","journal-title":"Bioinformatics"},{"key":"2026090323132741900_cit29","doi-asserted-by":"publisher","first-page":"W445","DOI":"10.1093\/nar\/gkq311","article-title":"HexServer:\nAn FFT-Based Protein Docking Server Powered by Graphics Processors","volume":"38","author":"Macindoe","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2026090323132741900_cit30","doi-asserted-by":"publisher","first-page":"W310","DOI":"10.1093\/nar\/gkl206","article-title":"GRAMM-X\nPublic Web Server for Protein-Protein Docking","volume":"34","author":"Tovchigrechko","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2026090323132741900_cit31","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0161879","article-title":"DockQ: A Quality Measure\nfor Protein-Protein Docking\nModels","volume":"11","author":"Basu","year":"2016","journal-title":"PLoS One"},{"key":"2026090323132741900_cit32","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1002\/prot.10381","article-title":"Critical\nAssessment\nof PRedicted Interactions. CAPRI: A Critical Assessment of PRedicted\nInteractions","volume":"52","author":"Janin","year":"2003","journal-title":"Proteins"},{"key":"2026090323132741900_cit33","doi-asserted-by":"publisher","first-page":"W229","DOI":"10.1093\/nar\/gkn186","article-title":"FireDock:\nA Web Server for Fast Interaction Refinement in Molecular Docking","volume":"36","author":"Mashiach","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2026090323132741900_cit34","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1186\/s12859-015-0572-6","article-title":"DOCKSCORE:\nA Webserver for Ranking\nProtein-Protein Docked Poses","volume":"16","author":"Malhotra","year":"2015","journal-title":"BMC Bioinformatics"},{"key":"2026090323132741900_cit35","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1002\/prot.25219","article-title":"New Additions\nto the ClusPro Server\nMotivated by CAPRI","volume":"85","author":"Vajda","year":"2017","journal-title":"Proteins"},{"key":"2026090323132741900_cit36","doi-asserted-by":"publisher","first-page":"883","DOI":"10.1038\/nprot.2010.32","article-title":"The HADDOCK\nWeb Server for Data-Driven Biomolecular Docking","volume":"5","author":"de Vries","year":"2010","journal-title":"Nat. Protoc."},{"key":"2026090323132741900_cit37","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1093\/intimm\/dxx077","article-title":"Toward Rational\nAntibody Design: Recent Advancements in Molecular Dynamics Simulations","volume":"30","author":"Yamashita","year":"2018","journal-title":"Int. Immunol."}],"container-title":["ACS Omega"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acsomega.0c00226","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/acsodf\/article-pdf\/5\/27\/16379\/67273088\/acsomega.0c00226.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/acsodf\/article-pdf\/5\/27\/16379\/67273088\/acsomega.0c00226.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T08:24:05Z","timestamp":1788510245000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/acsodf\/article\/5\/27\/16379\/505149\/Guidelines-To-Predict-Binding-Poses-of-Antibody"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,6,26]]},"references-count":37,"journal-issue":{"issue":"27","published-online":{"date-parts":[[2020,6,26]]},"published-print":{"date-parts":[[2020,7,14]]}},"URL":"https:\/\/doi.org\/10.1021\/acsomega.0c00226","relation":{},"ISSN":["2470-1343"],"issn-type":[{"value":"2470-1343","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,6,26]]}}}