{"id":"https://openalex.org/W4366743036","doi":"https://doi.org/10.1093/bioinformatics/btad212","title":"Pocket to concavity: a tool for the refinement of protein\u2013ligand binding site shape from alpha spheres","display_name":"Pocket to concavity: a tool for the refinement of protein\u2013ligand binding site shape from alpha spheres","publication_year":2023,"publication_date":"2023-04-01","ids":{"openalex":"https://openalex.org/W4366743036","doi":"https://doi.org/10.1093/bioinformatics/btad212","pmid":"https://pubmed.ncbi.nlm.nih.gov/37086438"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad212","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad212","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad212/50066624/btad212.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad212/50066624/btad212.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008000523","display_name":"Genki Kudo","orcid":"https://orcid.org/0000-0002-4727-7002"},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Genki Kudo","raw_affiliation_strings":["Physics Department, Graduate School of Pure and Applied Sciences, University of Tsukuba , Tsukuba, Ibaraki 305-8571, Japan"],"raw_orcid":"https://orcid.org/0000-0002-4727-7002","affiliations":[{"raw_affiliation_string":"Physics Department, Graduate School of Pure and Applied Sciences, University of Tsukuba , Tsukuba, Ibaraki 305-8571, Japan","institution_ids":["https://openalex.org/I146399215"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056724547","display_name":"Takumi Hirao","orcid":"https://orcid.org/0009-0006-4166-6150"},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takumi Hirao","raw_affiliation_strings":["Division of Biomedical Science, Faculty of Medicine, University of Tsukuba , Tsukuba, Ibaraki 305-8575, Japan","Master\u2019s Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba , Tsukuba, Ibaraki 305-8575, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Science, Faculty of Medicine, University of Tsukuba , Tsukuba, Ibaraki 305-8575, Japan","institution_ids":["https://openalex.org/I146399215"]},{"raw_affiliation_string":"Master\u2019s Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba , Tsukuba, Ibaraki 305-8575, Japan","institution_ids":["https://openalex.org/I146399215"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085299607","display_name":"Ryunosuke Yoshino","orcid":"https://orcid.org/0000-0002-5123-1349"},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ryunosuke Yoshino","raw_affiliation_strings":["Division of Biomedical Science, Faculty of Medicine, University of Tsukuba , Tsukuba, Ibaraki 305-8575, Japan","Transborder Medical Research Center, University of Tsukuba , Tsukuba, Ibaraki 305-8575, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Science, Faculty of Medicine, University of Tsukuba , Tsukuba, Ibaraki 305-8575, Japan","institution_ids":["https://openalex.org/I146399215"]},{"raw_affiliation_string":"Transborder Medical Research Center, University of Tsukuba , Tsukuba, Ibaraki 305-8575, Japan","institution_ids":["https://openalex.org/I146399215"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048994262","display_name":"Yasuteru Shigeta","orcid":"https://orcid.org/0000-0002-3219-6007"},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yasuteru Shigeta","raw_affiliation_strings":["Center for Computational Sciences, University of Tsukuba , Tsukuba, Ibaraki 305-8577, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Sciences, University of Tsukuba , Tsukuba, Ibaraki 305-8577, Japan","institution_ids":["https://openalex.org/I146399215"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027918582","display_name":"Takatsugu Hirokawa","orcid":"https://orcid.org/0000-0002-3180-5050"},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Takatsugu Hirokawa","raw_affiliation_strings":["Division of Biomedical Science, Faculty of Medicine, University of Tsukuba , Tsukuba, Ibaraki 305-8575, Japan","Transborder Medical Research Center, University of Tsukuba , Tsukuba, Ibaraki 305-8575, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Science, Faculty of Medicine, University of Tsukuba , Tsukuba, Ibaraki 305-8575, Japan","institution_ids":["https://openalex.org/I146399215"]},{"raw_affiliation_string":"Transborder Medical Research Center, University of Tsukuba , Tsukuba, Ibaraki 305-8575, Japan","institution_ids":["https://openalex.org/I146399215"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5008000523","https://openalex.org/A5027918582"],"corresponding_institution_ids":["https://openalex.org/I146399215"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.8073,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.7260901,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"39","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.3504999876022339,"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":0.3504999876022339,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.26570001244544983,"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/T11162","display_name":"Enzyme Structure and Function","score":0.040300000458955765,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/druggability","display_name":"Druggability","score":0.8363991975784302},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.7414318323135376},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5077860951423645},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.4742892384529114},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4647105932235718},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.41305190324783325},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3785043954849243},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3607199490070343},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.31155145168304443},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18292376399040222},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.09834587574005127},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09715664386749268}],"concepts":[{"id":"https://openalex.org/C10679952","wikidata":"https://www.wikidata.org/wiki/Q5308937","display_name":"Druggability","level":3,"score":0.8363991975784302},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.7414318323135376},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5077860951423645},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.4742892384529114},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4647105932235718},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.41305190324783325},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3785043954849243},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3607199490070343},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.31155145168304443},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18292376399040222},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.09834587574005127},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09715664386749268},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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":"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":"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":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad212","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad212","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad212/50066624/btad212.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37086438","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37086438","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:10148677","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10148677","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10148677/pdf/btad212.pdf","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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:tsukuba.repo.nii.ac.jp:02007806","is_oa":true,"landing_page_url":"http://hdl.handle.net/2241/0002007806","pdf_url":"https://tsukuba.repo.nii.ac.jp/record/2007806/files/Bioinformatics_39-4.pdf","source":{"id":"https://openalex.org/S4306402076","display_name":"Terrestrial Environment Research Center (University of Tsukuba)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I146399215","host_organization_name":"University of Tsukuba","host_organization_lineage":["https://openalex.org/I146399215"],"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":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad212","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad212","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad212/50066624/btad212.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.6499999761581421}],"awards":[{"id":"https://openalex.org/G8510248158","display_name":null,"funder_award_id":"JP22ama121029j0001","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"}],"funders":[{"id":"https://openalex.org/F4320311405","display_name":"Japan Agency for Medical Research and Development","ror":"https://ror.org/004rtk039"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4366743036.pdf"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W2031390939","https://openalex.org/W2081201773","https://openalex.org/W2105902442","https://openalex.org/W2164088236","https://openalex.org/W2805746983","https://openalex.org/W3177828909","https://openalex.org/W4285081903"],"related_works":["https://openalex.org/W2079953901","https://openalex.org/W1979414133","https://openalex.org/W2086380285","https://openalex.org/W2734414476","https://openalex.org/W3174574879","https://openalex.org/W4384197580","https://openalex.org/W1523514689","https://openalex.org/W2790525674","https://openalex.org/W2089928494","https://openalex.org/W4366743036"],"abstract_inverted_index":{"SUMMARY:":[0],"Understanding":[1],"the":[2,6,19,24,28,39,43,53,81,84,90,99,103],"binding":[3,21],"site":[4,22],"of":[5,23,42,83],"target":[7,25],"protein":[8,30],"is":[9,66,108,127,134],"essential":[10],"for":[11,52,110],"rational":[12],"drug":[13],"design.":[14],"Pocket":[15,61,124],"detection":[16],"software":[17],"predicts":[18],"ligand":[20],"protein;":[26],"however,":[27],"predicted":[29,55],"pockets":[31,54],"are":[32],"often":[33],"excessively":[34],"estimated":[35],"in":[36,116,136],"comparison":[37],"with":[38],"actual":[40],"volume":[41],"bound":[44,104],"ligands.":[45],"This":[46,132],"study":[47],"proposes":[48],"a":[49],"refinement":[50],"tool":[51,133],"by":[56],"an":[57],"alpha":[58],"sphere-based":[59],"approach,":[60],"to":[62,125],"Concavity":[63,126],"(P2C).":[64],"P2C":[65,107],"divided":[67],"into":[68],"two":[69],"modes:":[70],"Ligand-Free":[71],"(LF)":[72],"and":[73,86,112,138],"Ligand-Bound":[74],"(LB)":[75],"modes.":[76],"The":[77,95],"LF":[78],"mode":[79,97],"provides":[80],"shape":[82],"deep":[85,100],"druggable":[87],"concavity":[88,101],"where":[89],"core":[91],"scaffold":[92],"can":[93],"bind.":[94],"LB":[96],"searches":[98],"around":[102],"ligand.":[105],"Thus,":[106],"useful":[109],"identifying":[111],"designing":[113],"desirable":[114],"compounds":[115],"Structure-Based":[117],"Drug":[118],"Design":[119],"(SBDD).":[120],"AVAILABILITY":[121],"AND":[122],"IMPLEMENTATION:":[123],"freely":[128],"available":[129],"at":[130],"https://github.com/genki-kudo/Pocket-to-Concavity.":[131],"implemented":[135],"Python3":[137],"Fpocket2.":[139]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}