{"id":"https://openalex.org/W2106243683","doi":"https://doi.org/10.1093/nar/gkt457","title":"webPDBinder: a server for the identification of ligand binding sites on protein structures","display_name":"webPDBinder: a server for the identification of ligand binding sites on protein structures","publication_year":2013,"publication_date":"2013-06-03","ids":{"openalex":"https://openalex.org/W2106243683","doi":"https://doi.org/10.1093/nar/gkt457","mag":"2106243683","pmid":"https://pubmed.ncbi.nlm.nih.gov/23737450"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkt457","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt457","pdf_url":"https://academic.oup.com/nar/article-pdf/41/W1/W308/3866632/gkt457.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/41/W1/W308/3866632/gkt457.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085896954","display_name":"Valerio Bianchi","orcid":"https://orcid.org/0000-0001-9025-7923"},"institutions":[{"id":"https://openalex.org/I116067653","display_name":"University of Rome Tor Vergata","ror":"https://ror.org/02p77k626","country_code":"IT","type":"education","lineage":["https://openalex.org/I116067653"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Valerio Bianchi","raw_affiliation_strings":["Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy","Centre for Molecular Bioinformatics, Department of Biology, University of Rome \u2018Tor Vergata\u2019, Via della Ricerca Scientifica snc, 00133 Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy","institution_ids":["https://openalex.org/I116067653"]},{"raw_affiliation_string":"Centre for Molecular Bioinformatics, Department of Biology, University of Rome \u2018Tor Vergata\u2019, Via della Ricerca Scientifica snc, 00133 Rome, Italy","institution_ids":["https://openalex.org/I116067653"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046460960","display_name":"Iolanda Mangone","orcid":"https://orcid.org/0000-0002-6716-091X"},"institutions":[{"id":"https://openalex.org/I116067653","display_name":"University of Rome Tor Vergata","ror":"https://ror.org/02p77k626","country_code":"IT","type":"education","lineage":["https://openalex.org/I116067653"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Iolanda Mangone","raw_affiliation_strings":["Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy","Centre for Molecular Bioinformatics, Department of Biology, University of Rome \u2018Tor Vergata\u2019, Via della Ricerca Scientifica snc, 00133 Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy","institution_ids":["https://openalex.org/I116067653"]},{"raw_affiliation_string":"Centre for Molecular Bioinformatics, Department of Biology, University of Rome \u2018Tor Vergata\u2019, Via della Ricerca Scientifica snc, 00133 Rome, Italy","institution_ids":["https://openalex.org/I116067653"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044866381","display_name":"Fabrizio Ferr\u00e8","orcid":"https://orcid.org/0000-0003-2768-5305"},"institutions":[{"id":"https://openalex.org/I116067653","display_name":"University of Rome Tor Vergata","ror":"https://ror.org/02p77k626","country_code":"IT","type":"education","lineage":["https://openalex.org/I116067653"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Fabrizio Ferr\u00e8","raw_affiliation_strings":["Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy","Centre for Molecular Bioinformatics, Department of Biology, University of Rome \u2018Tor Vergata\u2019, Via della Ricerca Scientifica snc, 00133 Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy","institution_ids":["https://openalex.org/I116067653"]},{"raw_affiliation_string":"Centre for Molecular Bioinformatics, Department of Biology, University of Rome \u2018Tor Vergata\u2019, Via della Ricerca Scientifica snc, 00133 Rome, Italy","institution_ids":["https://openalex.org/I116067653"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089562631","display_name":"Manuela Helmer\u2010Citterich","orcid":"https://orcid.org/0000-0001-9530-7504"},"institutions":[{"id":"https://openalex.org/I116067653","display_name":"University of Rome Tor Vergata","ror":"https://ror.org/02p77k626","country_code":"IT","type":"education","lineage":["https://openalex.org/I116067653"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Manuela Helmer-Citterich","raw_affiliation_strings":["Centre for Molecular Bioinformatics, Department of Biology, University of Rome \u2018Tor Vergata\u2019, Via della Ricerca Scientifica snc, 00133 Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Molecular Bioinformatics, Department of Biology, University of Rome \u2018Tor Vergata\u2019, Via della Ricerca Scientifica snc, 00133 Rome, Italy","institution_ids":["https://openalex.org/I116067653"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058613175","display_name":"Gabriele Ausiello","orcid":"https://orcid.org/0000-0002-8075-5774"},"institutions":[{"id":"https://openalex.org/I116067653","display_name":"University of Rome Tor Vergata","ror":"https://ror.org/02p77k626","country_code":"IT","type":"education","lineage":["https://openalex.org/I116067653"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gabriele Ausiello","raw_affiliation_strings":["Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy","Centre for Molecular Bioinformatics, Department of Biology, University of Rome \u2018Tor Vergata\u2019, Via della Ricerca Scientifica snc, 00133 Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy","institution_ids":["https://openalex.org/I116067653"]},{"raw_affiliation_string":"Centre for Molecular Bioinformatics, Department of Biology, University of Rome \u2018Tor Vergata\u2019, Via della Ricerca Scientifica snc, 00133 Rome, Italy","institution_ids":["https://openalex.org/I116067653"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.1535,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.51359943,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"41","issue":"W1","first_page":"W308","last_page":"W313"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9973999857902527,"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"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9973999857902527,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9972000122070312,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9894000291824341,"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/binding-site","display_name":"Binding site","score":0.6738213896751404},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6603544354438782},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.6420312523841858},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5086634755134583},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.4835626780986786},{"id":"https://openalex.org/keywords/plasma-protein-binding","display_name":"Plasma protein binding","score":0.46924474835395813},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.45024538040161133},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4440632462501526},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.4143137037754059},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2778256833553314},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.26038891077041626},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.07168412208557129}],"concepts":[{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.6738213896751404},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6603544354438782},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.6420312523841858},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5086634755134583},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4835626780986786},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.46924474835395813},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.45024538040161133},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4440632462501526},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.4143137037754059},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2778256833553314},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.26038891077041626},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.07168412208557129},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkt457","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt457","pdf_url":"https://academic.oup.com/nar/article-pdf/41/W1/W308/3866632/gkt457.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:23737450","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23737450","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:art.torvergata.it:2108/77520","is_oa":true,"landing_page_url":"http://hdl.handle.net/2108/77520","pdf_url":"http://hdl.handle.net/2108/77520","source":{"id":"https://openalex.org/S4306400993","display_name":"Cineca Institutional Research Information System (Tor Vergata University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I116067653","host_organization_name":"University of Rome Tor Vergata","host_organization_lineage":["https://openalex.org/I116067653"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:cris.unibo.it:11585/372613","is_oa":false,"landing_page_url":"http://hdl.handle.net/11585/372613","pdf_url":null,"source":{"id":"https://openalex.org/S4306402579","display_name":"Archivio istituzionale della ricerca (Alma Mater Studiorum Universit\u00e0 di Bologna)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210117483","host_organization_name":"Istituto di Ematologia di Bologna","host_organization_lineage":["https://openalex.org/I4210117483"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:2686056","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3692056","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/nar/gkt457","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt457","pdf_url":"https://academic.oup.com/nar/article-pdf/41/W1/W308/3866632/gkt457.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.6899999976158142,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320323054","display_name":"Associazione Italiana per la Ricerca sul Cancro","ror":"https://ror.org/02g2x7380"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2106243683.pdf"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1508885706","https://openalex.org/W1585634379","https://openalex.org/W1968733906","https://openalex.org/W1994921798","https://openalex.org/W2001913949","https://openalex.org/W2003066987","https://openalex.org/W2004175162","https://openalex.org/W2007978853","https://openalex.org/W2017727500","https://openalex.org/W2024829861","https://openalex.org/W2044098591","https://openalex.org/W2045110975","https://openalex.org/W2047544230","https://openalex.org/W2047687868","https://openalex.org/W2055043387","https://openalex.org/W2066755794","https://openalex.org/W2073900163","https://openalex.org/W2090649877","https://openalex.org/W2090794687","https://openalex.org/W2091563009","https://openalex.org/W2096525273","https://openalex.org/W2098426148","https://openalex.org/W2100830941","https://openalex.org/W2101220662","https://openalex.org/W2122854841","https://openalex.org/W2123440974","https://openalex.org/W2123578540","https://openalex.org/W2126048802","https://openalex.org/W2126234813","https://openalex.org/W2126844417","https://openalex.org/W2128402268","https://openalex.org/W2132395520","https://openalex.org/W2137981491","https://openalex.org/W2141885858","https://openalex.org/W2144258433","https://openalex.org/W2154709258","https://openalex.org/W2162120660","https://openalex.org/W2162220273","https://openalex.org/W2169434145","https://openalex.org/W2171004217","https://openalex.org/W2313839046","https://openalex.org/W4230784961","https://openalex.org/W4320301318","https://openalex.org/W6635077098"],"related_works":["https://openalex.org/W3126783617","https://openalex.org/W2732388178","https://openalex.org/W3093468851","https://openalex.org/W4353055924","https://openalex.org/W2806488847","https://openalex.org/W2121688928","https://openalex.org/W2772651271","https://openalex.org/W4389958586","https://openalex.org/W2769925250","https://openalex.org/W4361279638"],"abstract_inverted_index":{"The":[0,37,78,163,174],"webPDBinder":[1,18,99],"(http://pdbinder.bio.uniroma2.it/PDBinder)":[2],"is":[3,49,71,114,130,149,165,176],"a":[4,15,20,24,31,54,74,146,167,171,177],"web":[5],"server":[6],"for":[7,57,132],"the":[8,43,46,61,66,69,91,95,105,111,134,139],"identification":[9],"of":[10,26,33,39,60,73,94,110,179],"small":[11],"ligand-binding":[12],"sites":[13,29],"in":[14,45,108,190],"protein":[16,21,63,97,141],"structure.":[17,173],"searches":[19],"structure":[22],"against":[23],"library":[25],"known":[27],"binding":[28,76,80,106,118,181],"and":[30,113,148,186,192],"collection":[32],"control":[34],"non-binding":[35],"pockets.":[36],"number":[38],"similarities":[40,155],"identified":[41],"with":[42,126,156,184],"residues":[44,81,102,183],"two":[47],"sets":[48],"then":[50],"used":[51],"to":[52,65,104,116,152],"derive":[53],"propensity":[55,185],"value":[56],"each":[58],"residue":[59,70],"query":[62,140],"associated":[64],"likelihood":[67],"that":[68],"part":[72],"ligand":[75,147],"site.":[77],"predicted":[79,180],"can":[82],"be":[83],"further":[84],"refined":[85],"using":[86],"conservation":[87,187],"scores":[88],"derived":[89],"from":[90,121,159],"multiple":[92],"alignment":[93],"PFAM":[96],"family.":[98],"correctly":[100],"identifies":[101],"belonging":[103],"site":[107],"77%":[109],"cases":[112,137],"able":[115],"identify":[117],"pockets":[119,158],"starting":[120],"holo":[122,160],"or":[123,170],"apo":[124],"structures":[125],"comparable":[127],"performances.":[128],"This":[129],"important":[131],"all":[133],"real":[135],"world":[136],"where":[138],"has":[142],"been":[143],"crystallized":[144],"without":[145],"also":[150],"difficult":[151],"obtain":[153],"clear":[154],"bound":[157],"pocket":[161,182],"libraries.":[162],"input":[164],"either":[166],"PDB":[168],"code":[169],"user-submitted":[172],"output":[175],"list":[178],"values":[188],"both":[189],"text":[191],"graphical":[193],"format.":[194]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
