{"id":"https://openalex.org/W2143099339","doi":"https://doi.org/10.1371/journal.pcbi.1000191","title":"Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes","display_name":"Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes","publication_year":2008,"publication_date":"2008-10-09","ids":{"openalex":"https://openalex.org/W2143099339","doi":"https://doi.org/10.1371/journal.pcbi.1000191","mag":"2143099339","pmid":"https://pubmed.ncbi.nlm.nih.gov/18846200"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000191","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000191","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000191&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000191&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100716873","display_name":"Yang Shen","orcid":"https://orcid.org/0000-0002-1703-7796"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yang Shen","raw_affiliation_strings":["Department of Biomedical Engineering, BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts, United States of America","BioMolecular Engineering Research Center, Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America","Center for Information and Systems Engineering, Boston University, Boston, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts, United States of America","institution_ids":[]},{"raw_affiliation_string":"BioMolecular Engineering Research Center, Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Center for Information and Systems Engineering, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075696701","display_name":"Ioannis Ch. Paschalidis","orcid":"https://orcid.org/0000-0002-3343-2913"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ioannis Ch. Paschalidis","raw_affiliation_strings":["Center for Information and Systems Engineering, Boston University, Boston, Massachusetts, United States of America","Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, United States of America","Division of Systems Engineering, Boston University, Boston, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Center for Information and Systems Engineering, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Division of Systems Engineering, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002097523","display_name":"Pirooz Vakili","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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pirooz Vakili","raw_affiliation_strings":["Center for Information and Systems Engineering, Boston University, Boston, Massachusetts, United States of America","Department of Mechanical Engineering, Boston University, Boston, Massachusetts, United States of America","Division of Systems Engineering, Boston University, Boston, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Center for Information and Systems Engineering, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Department of Mechanical Engineering, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Division of Systems Engineering, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"last","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"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sandor Vajda","raw_affiliation_strings":["BioMolecular Engineering Research Center, Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"BioMolecular Engineering Research Center, Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5032985635"],"corresponding_institution_ids":["https://openalex.org/I111088046"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.1065,"has_fulltext":true,"cited_by_count":43,"citation_normalized_percentile":{"value":0.77257531,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"4","issue":"10","first_page":"e1000191","last_page":"e1000191"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"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/T11162","display_name":"Enzyme Structure and Function","score":0.995199978351593,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9941999912261963,"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/docking","display_name":"Docking (animal)","score":0.6174493432044983},{"id":"https://openalex.org/keywords/macromolecular-docking","display_name":"Macromolecular docking","score":0.4300905466079712},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.3602149486541748},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3504941165447235},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3341562747955322},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3269686698913574},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3220616579055786},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27653273940086365},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.18630459904670715},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.12448948621749878}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.6174493432044983},{"id":"https://openalex.org/C116887118","wikidata":"https://www.wikidata.org/wiki/Q836685","display_name":"Macromolecular docking","level":3,"score":0.4300905466079712},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3602149486541748},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3504941165447235},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3341562747955322},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3269686698913574},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3220616579055786},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27653273940086365},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.18630459904670715},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.12448948621749878},{"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":9,"locations":[{"id":"doi:10.1371/journal.pcbi.1000191","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000191","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000191&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:18846200","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18846200","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.275.3265","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.275.3265","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/3d/f4/PLoS_Comput_Biol_2008_Oct_10_4(10)_e1000191.tar.gz","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1000191","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000191","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:doaj.org/article:ecbcce50a62547aa9b0b25bb3fdc851d","is_oa":true,"landing_page_url":"https://doaj.org/article/ecbcce50a62547aa9b0b25bb3fdc851d","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 4, Iss 10, p e1000191 (2008)","raw_type":"article"},{"id":"pmh:oai:open.bu.edu:2144/18022","is_oa":true,"landing_page_url":"https://hdl.handle.net/2144/18022","pdf_url":null,"source":{"id":"https://openalex.org/S4306402183","display_name":"OpenBU/Boston University Institutional Repository (Boston University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I111088046","host_organization_name":"Boston University","host_organization_lineage":["https://openalex.org/I111088046"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:open.bu.edu:2144/3041","is_oa":false,"landing_page_url":"https://hdl.handle.net/2144/3041","pdf_url":null,"source":{"id":"https://openalex.org/S4306402183","display_name":"OpenBU/Boston University Institutional Repository (Boston University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I111088046","host_organization_name":"Boston University","host_organization_lineage":["https://openalex.org/I111088046"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:open.bu.edu:2144/992","is_oa":false,"landing_page_url":"https://hdl.handle.net/2144/992","pdf_url":null,"source":{"id":"https://openalex.org/S4306402183","display_name":"OpenBU/Boston University Institutional Repository (Boston University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I111088046","host_organization_name":"Boston University","host_organization_lineage":["https://openalex.org/I111088046"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2538569","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2538569","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000191","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000191","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000191&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.9100000262260437}],"awards":[{"id":"https://openalex.org/G3749035419","display_name":null,"funder_award_id":"GM061867","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3880284734","display_name":null,"funder_award_id":"GM061867","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2143099339.pdf","grobid_xml":"https://content.openalex.org/works/W2143099339.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W174644880","https://openalex.org/W1483944095","https://openalex.org/W1561670438","https://openalex.org/W1578032121","https://openalex.org/W1967073510","https://openalex.org/W1969554454","https://openalex.org/W1973484256","https://openalex.org/W1975017420","https://openalex.org/W1979670056","https://openalex.org/W2014744153","https://openalex.org/W2018410079","https://openalex.org/W2019691413","https://openalex.org/W2027638447","https://openalex.org/W2036835637","https://openalex.org/W2037036397","https://openalex.org/W2039050554","https://openalex.org/W2045501270","https://openalex.org/W2045550557","https://openalex.org/W2048643046","https://openalex.org/W2058369753","https://openalex.org/W2065304353","https://openalex.org/W2065618512","https://openalex.org/W2078348971","https://openalex.org/W2084619201","https://openalex.org/W2092360980","https://openalex.org/W2094280270","https://openalex.org/W2097031841","https://openalex.org/W2105438341","https://openalex.org/W2110057983","https://openalex.org/W2111387452","https://openalex.org/W2112743424","https://openalex.org/W2113030357","https://openalex.org/W2113307443","https://openalex.org/W2115150990","https://openalex.org/W2115570685","https://openalex.org/W2123053665","https://openalex.org/W2126174597","https://openalex.org/W2127594538","https://openalex.org/W2129414710","https://openalex.org/W2130479394","https://openalex.org/W2133712572","https://openalex.org/W2135796990","https://openalex.org/W2138227733","https://openalex.org/W2143030588","https://openalex.org/W2149517992","https://openalex.org/W2162166182","https://openalex.org/W2165890129","https://openalex.org/W2167869241","https://openalex.org/W2171249995","https://openalex.org/W2171755502","https://openalex.org/W2296319761","https://openalex.org/W4230046802","https://openalex.org/W4285719527","https://openalex.org/W6665018949","https://openalex.org/W6670187722"],"related_works":["https://openalex.org/W2996908194","https://openalex.org/W2585040066","https://openalex.org/W2162380182","https://openalex.org/W3005126098","https://openalex.org/W2157273785","https://openalex.org/W2064383522","https://openalex.org/W2942988621","https://openalex.org/W3187431608","https://openalex.org/W1974422922","https://openalex.org/W4309353019"],"abstract_inverted_index":{"Similarly":[0],"to":[1,70,83,97,110,153,187,195,262],"protein":[2,211],"folding,":[3],"the":[4,24,42,54,80,100,111,131,139,143,148,156,159,162,177,196,219,232,237],"association":[5,200],"of":[6,23,37,44,53,74,113,130,138,142,147,158,198,206,231],"two":[7,132],"proteins":[8],"is":[9,106,223],"driven":[10],"by":[11,17,182],"a":[12,29,66,72,118,167,204,224,227],"free":[13,178,189,220],"energy":[14,39,76,169,179,190,221],"funnel,":[15],"determined":[16],"favorable":[18],"interactions":[19],"in":[20,41,99,216,226],"some":[21],"neighborhood":[22,230],"native":[25,233],"state.":[26],"We":[27,116],"describe":[28],"docking":[30,98,212,242],"method":[31],"based":[32],"on":[33],"stochastic":[34],"global":[35],"minimization":[36],"funnel-shaped":[38,93],"functions":[40,91],"space":[43,104,164,218],"rigid":[45],"body":[46],"motions":[47],"(SE(3))":[48],"while":[49,254],"accounting":[50],"for":[51,125,172,209],"flexibility":[52],"interface":[55,250],"side":[56],"chains.":[57],"The":[58,145],"method,":[59],"called":[60],"semi-definite":[61],"programming-based":[62],"underestimation":[63],"(SDU),":[64],"employs":[65],"general":[67],"quadratic":[68],"function":[69],"underestimate":[71],"set":[73],"local":[75,188],"minima":[77,191],"and":[78,102,134,192,235],"uses":[79,121],"resulting":[81],"underestimator":[82],"bias":[84],"further":[85],"sampling.":[86],"While":[87],"SDU":[88,238],"effectively":[89],"minimizes":[90],"with":[92,244],"basins,":[94],"its":[95],"application":[96],"rotational":[101],"translational":[103],"SE(3)":[105],"not":[107],"straightforward":[108],"due":[109],"geometry":[112],"that":[114,120,185,201,215,236],"space.":[115],"introduce":[117],"strategy":[119,239],"separate":[122],"independent":[123],"variables":[124],"side-chain":[126],"optimization,":[127],"center-to-center":[128,149],"distance":[129,150],"proteins,":[133],"five":[135],"angular":[136],"descriptors":[137],"relative":[140],"orientations":[141],"molecules.":[144],"removal":[146],"turns":[151],"out":[152],"vastly":[154],"improve":[155],"efficiency":[157,259],"search,":[160],"because":[161],"five-dimensional":[163],"now":[165],"exhibits":[166],"well-behaved":[168],"surface":[170,180],"suitable":[171],"underestimation.":[173],"This":[174],"algorithm":[175],"explores":[176],"spanned":[181],"encounter":[183],"complexes":[184],"correspond":[186],"shows":[193],"similarity":[194],"model":[197],"macromolecular":[199],"proceeds":[202],"through":[203],"series":[205],"collisions.":[207],"Results":[208],"standard":[210],"benchmarks":[213],"establish":[214],"this":[217],"landscape":[222],"funnel":[225],"reasonably":[228],"broad":[229],"state":[234],"can":[240],"generate":[241],"predictions":[243],"less":[245],"than":[246],"5":[247],"A":[248],"ligand":[249],"C(alpha)":[251],"root-mean-square":[252],"deviation":[253],"achieving":[255],"an":[256],"approximately":[257],"20-fold":[258],"gain":[260],"compared":[261],"Monte":[263],"Carlo":[264],"methods.":[265]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":5}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
