{"id":"https://openalex.org/W3116801402","doi":"https://doi.org/10.1093/bioinformatics/btaa805","title":"GRaSP: a graph-based residue neighborhood strategy to\u00a0predict binding sites","display_name":"GRaSP: a graph-based residue neighborhood strategy to\u00a0predict binding sites","publication_year":2020,"publication_date":"2020-09-08","ids":{"openalex":"https://openalex.org/W3116801402","doi":"https://doi.org/10.1093/bioinformatics/btaa805","mag":"3116801402","pmid":"https://pubmed.ncbi.nlm.nih.gov/33381849"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa805","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa805","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071320418","display_name":"Charles Abreu Santana","orcid":"https://orcid.org/0000-0001-7207-0858"},"institutions":[{"id":"https://openalex.org/I110200422","display_name":"Universidade Federal de Minas Gerais","ror":"https://ror.org/0176yjw32","country_code":"BR","type":"education","lineage":["https://openalex.org/I110200422"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Charles A Santana","raw_affiliation_strings":["Department of Biochemistry and Immunology","Department of Computer Science, Universidade Federal de Minas Gerais , Belo Horizonte 31270-901, Brazil"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Immunology","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, Universidade Federal de Minas Gerais , Belo Horizonte 31270-901, Brazil","institution_ids":["https://openalex.org/I110200422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021817826","display_name":"Sabrina de Azevedo Silveira","orcid":"https://orcid.org/0000-0002-4723-2349"},"institutions":[{"id":"https://openalex.org/I8165072","display_name":"Universidade Federal de Itajub\u00e1","ror":"https://ror.org/00235nr42","country_code":"BR","type":"education","lineage":["https://openalex.org/I8165072"]},{"id":"https://openalex.org/I146165071","display_name":"Universidade Federal de Vi\u00e7osa","ror":"https://ror.org/0409dgb37","country_code":"BR","type":"education","lineage":["https://openalex.org/I146165071"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Sabrina de A Silveira","raw_affiliation_strings":["Department of Computer Science, Universidade Federal de Vi\u00e7osa , Vi\u00e7osa 36570-900, Brazil","Institute of Technological Sciences (ICT), Advanced Campus at Itabira, Universidade Federal de Itajub\u00e1 , Itabira 35903-087, Brazil"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Universidade Federal de Vi\u00e7osa , Vi\u00e7osa 36570-900, Brazil","institution_ids":["https://openalex.org/I146165071"]},{"raw_affiliation_string":"Institute of Technological Sciences (ICT), Advanced Campus at Itabira, Universidade Federal de Itajub\u00e1 , Itabira 35903-087, Brazil","institution_ids":["https://openalex.org/I8165072"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030334085","display_name":"Jo\u00e3o Pedro Moraes","orcid":null},"institutions":[{"id":"https://openalex.org/I8165072","display_name":"Universidade Federal de Itajub\u00e1","ror":"https://ror.org/00235nr42","country_code":"BR","type":"education","lineage":["https://openalex.org/I8165072"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Jo\u00e3o P A Moraes","raw_affiliation_strings":["Institute of Technological Sciences (ICT), Advanced Campus at Itabira, Universidade Federal de Itajub\u00e1 , Itabira 35903-087, Brazil"],"affiliations":[{"raw_affiliation_string":"Institute of Technological Sciences (ICT), Advanced Campus at Itabira, Universidade Federal de Itajub\u00e1 , Itabira 35903-087, Brazil","institution_ids":["https://openalex.org/I8165072"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010423483","display_name":"Sandro Carvalho Izidoro","orcid":"https://orcid.org/0000-0001-5555-3321"},"institutions":[{"id":"https://openalex.org/I8165072","display_name":"Universidade Federal de Itajub\u00e1","ror":"https://ror.org/00235nr42","country_code":"BR","type":"education","lineage":["https://openalex.org/I8165072"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Sandro C Izidoro","raw_affiliation_strings":["Institute of Technological Sciences (ICT), Advanced Campus at Itabira, Universidade Federal de Itajub\u00e1 , Itabira 35903-087, Brazil"],"affiliations":[{"raw_affiliation_string":"Institute of Technological Sciences (ICT), Advanced Campus at Itabira, Universidade Federal de Itajub\u00e1 , Itabira 35903-087, Brazil","institution_ids":["https://openalex.org/I8165072"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069672238","display_name":"Raquel C. de Melo-Minardi","orcid":"https://orcid.org/0000-0001-5190-100X"},"institutions":[{"id":"https://openalex.org/I110200422","display_name":"Universidade Federal de Minas Gerais","ror":"https://ror.org/0176yjw32","country_code":"BR","type":"education","lineage":["https://openalex.org/I110200422"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Raquel C de Melo-Minardi","raw_affiliation_strings":["Department of Biochemistry and Immunology","Department of Computer Science, Universidade Federal de Minas Gerais , Belo Horizonte 31270-901, Brazil"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Immunology","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, Universidade Federal de Minas Gerais , Belo Horizonte 31270-901, Brazil","institution_ids":["https://openalex.org/I110200422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035707479","display_name":"Ant\u00f3nio J. M. Ribeiro","orcid":"https://orcid.org/0000-0002-2533-1231"},"institutions":[{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"funder","lineage":["https://openalex.org/I87048295"]},{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ant\u00f3nio J M Ribeiro","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 1SD, UK"],"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078919568","display_name":"Jonathan D. Tyzack","orcid":"https://orcid.org/0000-0003-4827-9023"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"funder","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jonathan D Tyzack","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 1SD, UK"],"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069444770","display_name":"Neera Borkakoti","orcid":"https://orcid.org/0000-0002-5878-1490"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"funder","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Neera Borkakoti","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 1SD, UK"],"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068874280","display_name":"Janet M. Thornton","orcid":"https://orcid.org/0000-0003-0824-4096"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"funder","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Janet M Thornton","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 1SD, UK"],"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5021817826"],"corresponding_institution_ids":["https://openalex.org/I146165071","https://openalex.org/I8165072"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.5878,"has_fulltext":false,"cited_by_count":31,"citation_normalized_percentile":{"value":0.87566809,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"36","issue":"Supplement_2","first_page":"i726","last_page":"i734"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9983999729156494,"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":0.9983999729156494,"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":0.9980000257492065,"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/T12505","display_name":"Peptidase Inhibition and Analysis","score":0.9908000230789185,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/grasp","display_name":"GRASP","score":0.8236887454986572},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6071212291717529},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5368870496749878},{"id":"https://openalex.org/keywords/residue","display_name":"Residue (chemistry)","score":0.5298430919647217},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37363386154174805},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.26839447021484375},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2579565644264221},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.13288342952728271},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10301047563552856}],"concepts":[{"id":"https://openalex.org/C171268870","wikidata":"https://www.wikidata.org/wiki/Q1486676","display_name":"GRASP","level":2,"score":0.8236887454986572},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6071212291717529},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5368870496749878},{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.5298430919647217},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37363386154174805},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.26839447021484375},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2579565644264221},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.13288342952728271},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10301047563552856}],"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":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018737","descriptor_name":"Hand Strength","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018737","descriptor_name":"Hand Strength","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018737","descriptor_name":"Hand Strength","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaa805","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa805","pdf_url":null,"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:33381849","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33381849","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}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Sustainable cities and communities","score":0.5899999737739563,"id":"https://metadata.un.org/sdg/11"}],"awards":[{"id":"https://openalex.org/G1382761819","display_name":null,"funder_award_id":"23038.004007/2014-82","funder_id":"https://openalex.org/F4320321091","funder_display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior"},{"id":"https://openalex.org/G6074959722","display_name":null,"funder_award_id":"051/2013","funder_id":"https://openalex.org/F4320321091","funder_display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior"}],"funders":[{"id":"https://openalex.org/F4320313288","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52"},{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320322980","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de Minas Gerais","ror":"https://ror.org/00nc55f03"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W1927265873","https://openalex.org/W1964640688","https://openalex.org/W1983194490","https://openalex.org/W2000588380","https://openalex.org/W2018661561","https://openalex.org/W2056132907","https://openalex.org/W2059215264","https://openalex.org/W2062884696","https://openalex.org/W2078176948","https://openalex.org/W2081556853","https://openalex.org/W2090794687","https://openalex.org/W2101234009","https://openalex.org/W2104812418","https://openalex.org/W2114850508","https://openalex.org/W2115336138","https://openalex.org/W2123440974","https://openalex.org/W2126048802","https://openalex.org/W2126754352","https://openalex.org/W2132395520","https://openalex.org/W2140538197","https://openalex.org/W2144258433","https://openalex.org/W2146233784","https://openalex.org/W2149095014","https://openalex.org/W2154657801","https://openalex.org/W2156368280","https://openalex.org/W2158964183","https://openalex.org/W2164088236","https://openalex.org/W2180527714","https://openalex.org/W2211863317","https://openalex.org/W2325034207","https://openalex.org/W2380593613","https://openalex.org/W2609293186","https://openalex.org/W2617750324","https://openalex.org/W2740924709","https://openalex.org/W2745395435","https://openalex.org/W2762787945","https://openalex.org/W2767813457","https://openalex.org/W2770647690","https://openalex.org/W2804171113","https://openalex.org/W2807540482","https://openalex.org/W2887981960","https://openalex.org/W2898402099","https://openalex.org/W2949301282","https://openalex.org/W2950200056","https://openalex.org/W2955341169","https://openalex.org/W2980948514","https://openalex.org/W3136918052","https://openalex.org/W6675354045"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2163296013","https://openalex.org/W2743859443","https://openalex.org/W2326995835","https://openalex.org/W165915117","https://openalex.org/W2059402478","https://openalex.org/W2123347777","https://openalex.org/W2963326767"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-12T08:34:05.389933","created_date":"2025-10-10T00:00:00"}