{"id":"https://openalex.org/W2168565692","doi":"https://doi.org/10.1093/bioinformatics/btr717","title":"Small-molecule inhibitor starting points learned from protein\u2013protein interaction inhibitor structure","display_name":"Small-molecule inhibitor starting points learned from protein\u2013protein interaction inhibitor structure","publication_year":2011,"publication_date":"2011-12-30","ids":{"openalex":"https://openalex.org/W2168565692","doi":"https://doi.org/10.1093/bioinformatics/btr717","mag":"2168565692","pmid":"https://pubmed.ncbi.nlm.nih.gov/22210869"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr717","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr717","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/6/784/16910635/btr717.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/28/6/784/16910635/btr717.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040700924","display_name":"David Ryan Koes","orcid":"https://orcid.org/0000-0002-6892-6614"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David Ryan Koes","raw_affiliation_strings":["Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023869904","display_name":"Carlos J. Camacho","orcid":"https://orcid.org/0000-0003-1741-8529"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carlos J. Camacho","raw_affiliation_strings":["Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5040700924"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":7.2182,"has_fulltext":true,"cited_by_count":60,"citation_normalized_percentile":{"value":0.97735806,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"28","issue":"6","first_page":"784","last_page":"791"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9855999946594238,"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/T13326","display_name":"Biochemical and Structural Characterization","score":0.9664000272750854,"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/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.8677866458892822},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.7598583698272705},{"id":"https://openalex.org/keywords/small-molecule","display_name":"Small molecule","score":0.6602619886398315},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.5751070976257324},{"id":"https://openalex.org/keywords/training-set","display_name":"Training set","score":0.574752151966095},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.5406252145767212},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5318887829780579},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5146847367286682},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.5074607729911804},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.5039371848106384},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.4682392179965973},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.4296759068965912},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.3670642077922821},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.35968807339668274},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3417873978614807},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.30651143193244934},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.28417038917541504},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2756010890007019},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21743616461753845}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.8677866458892822},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.7598583698272705},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.6602619886398315},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.5751070976257324},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.574752151966095},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.5406252145767212},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5318887829780579},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5146847367286682},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.5074607729911804},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.5039371848106384},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.4682392179965973},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.4296759068965912},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.3670642077922821},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.35968807339668274},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3417873978614807},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.30651143193244934},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.28417038917541504},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2756010890007019},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21743616461753845}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btr717","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr717","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/6/784/16910635/btr717.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:22210869","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22210869","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:pubmedcentral.nih.gov:3307105","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3307105","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr717","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr717","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/6/784/16910635/btr717.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":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2168565692.pdf","grobid_xml":"https://content.openalex.org/works/W2168565692.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W1510526001","https://openalex.org/W1555195606","https://openalex.org/W1964364336","https://openalex.org/W1965582988","https://openalex.org/W1969370763","https://openalex.org/W1972821149","https://openalex.org/W1979414133","https://openalex.org/W1985222378","https://openalex.org/W1985711767","https://openalex.org/W1989181256","https://openalex.org/W1993046136","https://openalex.org/W1998063251","https://openalex.org/W1999390565","https://openalex.org/W2001709898","https://openalex.org/W2002303652","https://openalex.org/W2013600324","https://openalex.org/W2019951137","https://openalex.org/W2024894759","https://openalex.org/W2029112828","https://openalex.org/W2030648131","https://openalex.org/W2033893117","https://openalex.org/W2038555943","https://openalex.org/W2041008131","https://openalex.org/W2055043387","https://openalex.org/W2056169996","https://openalex.org/W2058527555","https://openalex.org/W2066143642","https://openalex.org/W2067865468","https://openalex.org/W2083441741","https://openalex.org/W2096864392","https://openalex.org/W2102791444","https://openalex.org/W2103568877","https://openalex.org/W2114801649","https://openalex.org/W2115156437","https://openalex.org/W2116099439","https://openalex.org/W2116211618","https://openalex.org/W2118507670","https://openalex.org/W2121166097","https://openalex.org/W2121926265","https://openalex.org/W2127506367","https://openalex.org/W2130167865","https://openalex.org/W2136206140","https://openalex.org/W2136224545","https://openalex.org/W2137015675","https://openalex.org/W2137991504","https://openalex.org/W2141340736","https://openalex.org/W2141624700","https://openalex.org/W2146465875","https://openalex.org/W2150381702","https://openalex.org/W2161732286","https://openalex.org/W2162166182","https://openalex.org/W2162402626","https://openalex.org/W6630424276","https://openalex.org/W6655239331","https://openalex.org/W6680215210","https://openalex.org/W6680899909"],"related_works":["https://openalex.org/W1714666523","https://openalex.org/W2158819124","https://openalex.org/W2320246267","https://openalex.org/W2171716824","https://openalex.org/W2890221005","https://openalex.org/W2338762894","https://openalex.org/W2168565692","https://openalex.org/W2153819507","https://openalex.org/W2951715242","https://openalex.org/W2002622959"],"abstract_inverted_index":{"We":[0],"extract":[1],"Small-Molecule":[2],"Inhibitor":[3],"Starting":[4],"Points":[5],"(SMISPs)":[6],"from":[7],"protein-ligand":[8],"and":[9,31,48],"protein-protein":[10],"complexes":[11],"in":[12,57],"the":[13,58],"Protein":[14],"Data":[15],"Bank":[16],"(PDB).":[17],"These":[18],"SMISPs":[19,51],"are":[20],"used":[21],"to":[22,34,74],"train":[23],"two":[24],"distinct":[25],"classifiers,":[26],"a":[27],"support":[28],"vector":[29],"machine":[30],"an":[32],"easy":[33],"interpret":[35],"exhaustive":[36],"rule":[37],"classifier.":[38],"Both":[39],"classifiers":[40],"achieve":[41],"better":[42],"than":[43],"70%":[44],"leave-one-complex-out":[45],"cross-validation":[46],"accuracy":[47],"correctly":[49],"predict":[50],"of":[52,68],"known":[53],"PPI":[54],"inhibitors":[55],"not":[56],"training":[59],"set.":[60],"A":[61],"PDB-wide":[62],"analysis":[63],"suggests":[64],"that":[65],"nearly":[66],"half":[67],"all":[69],"PPIs":[70],"may":[71],"be":[72],"susceptible":[73],"small-molecule":[75],"inhibition.":[76]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":6},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":10},{"year":2012,"cited_by_count":6}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
