{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T23:02:03Z","timestamp":1773702123611,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: An effective docking algorithm for antibody\u2013protein antigen complex prediction is an important first step toward design of biologics and vaccines. We have recently developed a new class of knowledge-based interaction potentials called Decoys as the Reference State (DARS) and incorporated DARS into the docking program PIPER based on the fast Fourier transform correlation approach. Although PIPER was the best performer in the latest rounds of the CAPRI protein docking experiment, it is much less accurate for docking antibody\u2013protein antigen pairs than other types of complexes, in spite of incorporating sequence-based information on the location of the paratope. Analysis of antibody\u2013protein antigen complexes has revealed an inherent asymmetry within these interfaces. Specifically, phenylalanine, tryptophan and tyrosine residues highly populate the paratope of the antibody but not the epitope of the antigen.<\/jats:p>\n               <jats:p>Results: Since this asymmetry cannot be adequately modeled using a symmetric pairwise potential, we have removed the usual assumption of symmetry. Interaction statistics were extracted from antibody\u2013protein complexes under the assumption that a particular atom on the antibody is different from the same atom on the antigen protein. The use of the new potential significantly improves the performance of docking for antibody\u2013protein antigen complexes, even without any sequence information on the location of the paratope. We note that the asymmetric potential captures the effects of the multi-body interactions inherent to the complex environment in the antibody\u2013protein antigen interface.<\/jats:p>\n               <jats:p>Availability: The method is implemented in the ClusPro protein docking server, available at http:\/\/cluspro.bu.edu.<\/jats:p>\n               <jats:p>Contact: \u00a0midas@bu.edu or vajda@bu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts493","type":"journal-article","created":{"date-parts":[[2012,10,10]],"date-time":"2012-10-10T10:43:38Z","timestamp":1349865818000},"page":"2608-2614","source":"Crossref","is-referenced-by-count":188,"title":["Application of asymmetric statistical potentials to antibody\u2013protein docking"],"prefix":"10.1093","volume":"28","author":[{"given":"Ryan","family":"Brenke","sequence":"first","affiliation":[{"name":"1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel"}]},{"given":"David R.","family":"Hall","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel"}]},{"given":"Gwo-Yu","family":"Chuang","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel"}]},{"given":"Stephen R.","family":"Comeau","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel"}]},{"given":"Tanggis","family":"Bohnuud","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel"}]},{"given":"Dmitri","family":"Beglov","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel"}]},{"given":"Ora","family":"Schueler-Furman","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel"}]},{"given":"Sandor","family":"Vajda","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel"}]},{"given":"Dima","family":"Kozakov","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel"}]}],"member":"286","published-online":{"date-parts":[[2012,10,6]]},"reference":[{"key":"2023012513140784200_bts493-B1","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1002\/prot.10389","article-title":"ZDOCK: an initial-stage protein-docking algorithm","volume":"52","author":"Chen","year":"2003","journal-title":"Proteins"},{"key":"2023012513140784200_bts493-B2","doi-asserted-by":"crossref","first-page":"4217","DOI":"10.1529\/biophysj.108.135814","article-title":"DARS (Decoys as the Reference State) potentials for protein\u2013protein docking","volume":"95","author":"Chuang","year":"2008","journal-title":"Biophys. 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