{"id":"https://openalex.org/W2099367604","doi":"https://doi.org/10.1093/bioinformatics/bts493","title":"Application of asymmetric statistical potentials to antibody\u2013protein docking","display_name":"Application of asymmetric statistical potentials to antibody\u2013protein docking","publication_year":2012,"publication_date":"2012-10-06","ids":{"openalex":"https://openalex.org/W2099367604","doi":"https://doi.org/10.1093/bioinformatics/bts493","mag":"2099367604","pmid":"https://pubmed.ncbi.nlm.nih.gov/23053206"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts493","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts493","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/20/2608/48874148/bioinformatics_28_20_2608.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/20/2608/48874148/bioinformatics_28_20_2608.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027646171","display_name":"Ryan Brenke","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]},{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL","US"],"is_corresponding":true,"raw_author_name":"Ryan Brenke","raw_affiliation_strings":["1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel","institution_ids":["https://openalex.org/I111088046","https://openalex.org/I197251160"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102709739","display_name":"David R. Hall","orcid":"https://orcid.org/0000-0002-5333-6136"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]},{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL","US"],"is_corresponding":true,"raw_author_name":"David R. Hall","raw_affiliation_strings":["1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel","institution_ids":["https://openalex.org/I111088046","https://openalex.org/I197251160"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069049986","display_name":"Gwo\u2010Yu Chuang","orcid":"https://orcid.org/0000-0003-0375-1013"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]},{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL","US"],"is_corresponding":true,"raw_author_name":"Gwo-Yu Chuang","raw_affiliation_strings":["1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel","institution_ids":["https://openalex.org/I111088046","https://openalex.org/I197251160"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038298924","display_name":"Stephen R. Comeau","orcid":"https://orcid.org/0000-0003-4281-2026"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]},{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL","US"],"is_corresponding":false,"raw_author_name":"Stephen R. Comeau","raw_affiliation_strings":["1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel","institution_ids":["https://openalex.org/I111088046","https://openalex.org/I197251160"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008164121","display_name":"Tanggis Bohnuud","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]},{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL","US"],"is_corresponding":false,"raw_author_name":"Tanggis Bohnuud","raw_affiliation_strings":["1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel","institution_ids":["https://openalex.org/I111088046","https://openalex.org/I197251160"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005150199","display_name":"Dmitri Beglov","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]},{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL","US"],"is_corresponding":false,"raw_author_name":"Dmitri Beglov","raw_affiliation_strings":["1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel","institution_ids":["https://openalex.org/I111088046","https://openalex.org/I197251160"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034150494","display_name":"Ora Schueler\u2010Furman","orcid":"https://orcid.org/0000-0002-1624-0362"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]},{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL","US"],"is_corresponding":false,"raw_author_name":"Ora Schueler-Furman","raw_affiliation_strings":["1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel","institution_ids":["https://openalex.org/I111088046","https://openalex.org/I197251160"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032985635","display_name":"S\u00e1ndor Vajda","orcid":"https://orcid.org/0000-0003-1540-8220"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]},{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL","US"],"is_corresponding":true,"raw_author_name":"Sandor Vajda","raw_affiliation_strings":["1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel","institution_ids":["https://openalex.org/I111088046","https://openalex.org/I197251160"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060147489","display_name":"Dima Kozakov","orcid":"https://orcid.org/0000-0003-0464-4500"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]},{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL","US"],"is_corresponding":true,"raw_author_name":"Dima Kozakov","raw_affiliation_strings":["1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biomedical Engineering, Boston University, Boston, MA, USA, and 2Department of Microbiology and Molecular Genetics, The Hebrew University, Jerusalem, Israel","institution_ids":["https://openalex.org/I111088046","https://openalex.org/I197251160"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5027646171","https://openalex.org/A5032985635","https://openalex.org/A5060147489","https://openalex.org/A5069049986","https://openalex.org/A5102709739"],"corresponding_institution_ids":["https://openalex.org/I111088046","https://openalex.org/I197251160"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.7007,"has_fulltext":true,"cited_by_count":213,"citation_normalized_percentile":{"value":0.90943945,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"28","issue":"20","first_page":"2608","last_page":"2614"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.5586000084877014,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.5586000084877014,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.28450000286102295,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.03180000185966492,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/paratope","display_name":"Paratope","score":0.9281398057937622},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.7980853319168091},{"id":"https://openalex.org/keywords/macromolecular-docking","display_name":"Macromolecular docking","score":0.742161750793457},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5997589826583862},{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.5323536396026611},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.5187735557556152},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4940967857837677},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4901467263698578},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.4559829831123352},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.4388415515422821},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.38337209820747375},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.38259416818618774},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23672401905059814},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2160351276397705},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.17309686541557312},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.10127869248390198}],"concepts":[{"id":"https://openalex.org/C9086966","wikidata":"https://www.wikidata.org/wiki/Q489135","display_name":"Paratope","level":4,"score":0.9281398057937622},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7980853319168091},{"id":"https://openalex.org/C116887118","wikidata":"https://www.wikidata.org/wiki/Q836685","display_name":"Macromolecular docking","level":3,"score":0.742161750793457},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5997589826583862},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.5323536396026611},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.5187735557556152},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4940967857837677},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4901467263698578},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.4559829831123352},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.4388415515422821},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.38337209820747375},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.38259416818618774},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23672401905059814},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2160351276397705},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.17309686541557312},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.10127869248390198},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000936","descriptor_name":"Antigen-Antibody Complex","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000936","descriptor_name":"Antigen-Antibody Complex","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000936","descriptor_name":"Antigen-Antibody Complex","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000936","descriptor_name":"Antigen-Antibody Complex","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000936","descriptor_name":"Antigen-Antibody Complex","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000936","descriptor_name":"Antigen-Antibody Complex","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005583","descriptor_name":"Fourier Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005583","descriptor_name":"Fourier Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005583","descriptor_name":"Fourier Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bts493","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts493","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/20/2608/48874148/bioinformatics_28_20_2608.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23053206","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23053206","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:2787190","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3467743","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts493","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts493","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/20/2608/48874148/bioinformatics_28_20_2608.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G479164073","display_name":"Interactions between Turbulence and Waves: Kinetic Approach","funder_award_id":"2009418","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G49992848","display_name":null,"funder_award_id":"GM93147","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G700947639","display_name":null,"funder_award_id":"R01-GM061867","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G748954555","display_name":null,"funder_award_id":"R01 GM093147","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8483106597","display_name":null,"funder_award_id":"GM61867","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8978210475","display_name":"ABI Development: Refinement Algorithms and Server for Protein Docking","funder_award_id":"1147082","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2099367604.pdf","grobid_xml":"https://content.openalex.org/works/W2099367604.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W174644880","https://openalex.org/W1480478557","https://openalex.org/W1975017420","https://openalex.org/W2001956250","https://openalex.org/W2025120281","https://openalex.org/W2026344481","https://openalex.org/W2027403155","https://openalex.org/W2036808217","https://openalex.org/W2070623622","https://openalex.org/W2075770210","https://openalex.org/W2091734240","https://openalex.org/W2097031841","https://openalex.org/W2101395824","https://openalex.org/W2102312699","https://openalex.org/W2111387452","https://openalex.org/W2112743424","https://openalex.org/W2128039232","https://openalex.org/W2131063642","https://openalex.org/W2133712572","https://openalex.org/W2137736208","https://openalex.org/W2145154167","https://openalex.org/W2158781610","https://openalex.org/W2162682281","https://openalex.org/W2165271176","https://openalex.org/W2167300514","https://openalex.org/W2171249995","https://openalex.org/W2915344963"],"related_works":["https://openalex.org/W1503631901","https://openalex.org/W2099367604","https://openalex.org/W4229020575","https://openalex.org/W3187431608","https://openalex.org/W2049053970","https://openalex.org/W2155796229","https://openalex.org/W2342853224","https://openalex.org/W2963060696","https://openalex.org/W1971722050","https://openalex.org/W1644470444"],"abstract_inverted_index":{"MOTIVATION:":[0],"An":[1],"effective":[2],"docking":[3,44,69,77,190,238],"algorithm":[4],"for":[5,76,191],"antibody-protein":[6,78,100,157,192,226],"antigen":[7,79,101,177,193,227],"complex":[8,222],"prediction":[9],"is":[10,72,169,232],"an":[11,105],"important":[12],"first":[13],"step":[14],"toward":[15],"design":[16],"of":[17,28,65,84,88,95,99,121,128,150,181,189,203,215],"biologics":[18],"and":[19,39,114],"vaccines.":[20],"We":[21,206],"have":[22,145],"recently":[23],"developed":[24],"a":[25,140,163],"new":[26,183],"class":[27],"knowledge-based":[29],"interaction":[30],"potentials":[31],"called":[32],"Decoys":[33],"as":[34],"the":[35,43,49,58,62,66,93,96,119,122,126,129,147,160,167,172,176,182,187,201,204,209,213,216,221,225,235],"Reference":[36],"State":[37],"(DARS)":[38],"incorporated":[40],"DARS":[41],"into":[42],"program":[45],"PIPER":[46,56],"based":[47],"on":[48,92,166,175,200],"fast":[50],"Fourier":[51],"transform":[52],"correlation":[53],"approach.":[54],"Although":[55],"was":[57],"best":[59],"performer":[60],"in":[61,86,224,234],"latest":[63],"rounds":[64],"CAPRI":[67],"protein":[68,237],"experiment,":[70],"it":[71],"much":[73],"less":[74],"accurate":[75],"pairs":[80],"than":[81],"other":[82],"types":[83],"complexes,":[85,194],"spite":[87],"incorporating":[89],"sequence-based":[90],"information":[91,199],"location":[94,202],"paratope.":[97,205],"Analysis":[98],"complexes":[102,158],"has":[103],"revealed":[104],"inherent":[106,219],"asymmetry":[107,134],"within":[108],"these":[109],"interfaces.":[110],"Specifically,":[111],"phenylalanine,":[112],"tryptophan":[113],"tyrosine":[115],"residues":[116],"highly":[117],"populate":[118],"paratope":[120],"antibody":[123,168],"but":[124],"not":[125],"epitope":[127],"antigen.":[130],"RESULTS:":[131],"Since":[132],"this":[133],"cannot":[135],"be":[136],"adequately":[137],"modeled":[138],"using":[139],"symmetric":[141],"pairwise":[142],"potential,":[143],"we":[144],"removed":[146],"usual":[148],"assumption":[149,161],"symmetry.":[151],"Interaction":[152],"statistics":[153],"were":[154],"extracted":[155],"from":[156,171],"under":[159],"that":[162,208],"particular":[164],"atom":[165,174],"different":[170],"same":[173],"protein.":[178],"The":[179,230],"use":[180],"potential":[184,211],"significantly":[185],"improves":[186],"performance":[188],"even":[195],"without":[196],"any":[197],"sequence":[198],"note":[207],"asymmetric":[210],"captures":[212],"effects":[214],"multi-body":[217],"interactions":[218],"to":[220],"environment":[223],"interface.":[228],"AVAILABILITY:":[229],"method":[231],"implemented":[233],"ClusPro":[236],"server,":[239],"available":[240],"at":[241],"http://cluspro.bu.edu.":[242]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":20},{"year":2024,"cited_by_count":27},{"year":2023,"cited_by_count":21},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":23},{"year":2020,"cited_by_count":20},{"year":2019,"cited_by_count":18},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":14},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":6}],"updated_date":"2026-08-05T07:39:15.569665","created_date":"2025-10-10T00:00:00"}