{"id":"https://openalex.org/W1966388405","doi":"https://doi.org/10.1007/s10822-009-9277-0","title":"Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: II. Case studies and applications","display_name":"Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: II. Case studies and applications","publication_year":2009,"publication_date":"2009-06-22","ids":{"openalex":"https://openalex.org/W1966388405","doi":"https://doi.org/10.1007/s10822-009-9277-0","mag":"1966388405","pmid":"https://pubmed.ncbi.nlm.nih.gov/19548090"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-009-9277-0","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-009-9277-0","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5052974651","display_name":"Deepak Bandyopadhyay","orcid":"https://orcid.org/0000-0002-8747-369X"},"institutions":[{"id":"https://openalex.org/I4210156610","display_name":"GlaxoSmithKline (Netherlands)","ror":"https://ror.org/05atcw115","country_code":"NL","type":"company","lineage":["https://openalex.org/I188950975","https://openalex.org/I4210156610"]},{"id":"https://openalex.org/I4210114143","display_name":"GlaxoSmithKline (United States)","ror":"https://ror.org/025vn3989","country_code":"US","type":"company","lineage":["https://openalex.org/I188950975","https://openalex.org/I4210114143"]}],"countries":["NL","US"],"is_corresponding":true,"raw_author_name":"Deepak Bandyopadhyay","raw_affiliation_strings":["GlaxoSmithKline, Collegeville, PA, USA. deepak.2.bandyopadhyay@gsk.com","GlaxoSmithKline"],"affiliations":[{"raw_affiliation_string":"GlaxoSmithKline, Collegeville, PA, USA. deepak.2.bandyopadhyay@gsk.com","institution_ids":["https://openalex.org/I4210114143"]},{"raw_affiliation_string":"GlaxoSmithKline","institution_ids":["https://openalex.org/I4210156610"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107809276","display_name":"Jun Huan","orcid":null},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jun Huan","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS, USA","University of Kansas"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS, USA","institution_ids":["https://openalex.org/I146416000"]},{"raw_affiliation_string":"University of Kansas","institution_ids":["https://openalex.org/I146416000"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047002646","display_name":"Jan M. Prins","orcid":"https://orcid.org/0000-0002-5415-8933"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jan Prins","raw_affiliation_strings":["Department of Computer Science, University of North Carolina, CB#3175 Sitterson Hall, Chapel Hill, NC, USA","Dept. of Computer Science, University of North Carolina-Chapel Hill, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of North Carolina, CB#3175 Sitterson Hall, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Dept. of Computer Science, University of North Carolina-Chapel Hill, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074061303","display_name":"Jack Snoeyink","orcid":"https://orcid.org/0000-0002-3887-4008"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jack Snoeyink","raw_affiliation_strings":["Department of Computer Science, University of North Carolina, CB#3175 Sitterson Hall, Chapel Hill, NC, USA","Dept. of Computer Science, University of North Carolina-Chapel Hill, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of North Carolina, CB#3175 Sitterson Hall, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Dept. of Computer Science, University of North Carolina-Chapel Hill, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100392089","display_name":"Wei Wang","orcid":"https://orcid.org/0000-0002-8180-2886"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Wang","raw_affiliation_strings":["Department of Computer Science, University of North Carolina, CB#3175 Sitterson Hall, Chapel Hill, NC, USA","University of North Carolina"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of North Carolina, CB#3175 Sitterson Hall, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"University of North Carolina","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078536199","display_name":"Alexander Tropsha","orcid":"https://orcid.org/0000-0003-3802-8896"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander Tropsha","raw_affiliation_strings":["School of Pharmacy, University of North Carolina, CB#7360 Beard Hall, Chapel Hill, NC, USA","School of Pharmacy, University of North Carolina, Chapel Hill, USA"],"affiliations":[{"raw_affiliation_string":"School of Pharmacy, University of North Carolina, CB#7360 Beard Hall, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"School of Pharmacy, University of North Carolina, Chapel Hill, USA","institution_ids":["https://openalex.org/I114027177"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5052974651"],"corresponding_institution_ids":["https://openalex.org/I4210114143","https://openalex.org/I4210156610"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":null,"fwci":0.671,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.67828669,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"23","issue":"11","first_page":"785","last_page":"797"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9991000294685364,"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":0.9991000294685364,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.996999979019165,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9959999918937683,"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/inference","display_name":"Inference","score":0.7758098840713501},{"id":"https://openalex.org/keywords/structural-genomics","display_name":"Structural genomics","score":0.665966808795929},{"id":"https://openalex.org/keywords/protein-family","display_name":"Protein family","score":0.5781572461128235},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5631424188613892},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5191689729690552},{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"Protein function prediction","score":0.5140422582626343},{"id":"https://openalex.org/keywords/structural-motif","display_name":"Structural motif","score":0.5014150142669678},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4776115119457245},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4647499918937683},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41644641757011414},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.41349658370018005},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.4129725992679596},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.408551424741745},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.343824177980423},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3118894100189209},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22430625557899475},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.104522705078125}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7758098840713501},{"id":"https://openalex.org/C192772702","wikidata":"https://www.wikidata.org/wiki/Q2583975","display_name":"Structural genomics","level":3,"score":0.665966808795929},{"id":"https://openalex.org/C171897839","wikidata":"https://www.wikidata.org/wiki/Q417841","display_name":"Protein family","level":3,"score":0.5781572461128235},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5631424188613892},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5191689729690552},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.5140422582626343},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.5014150142669678},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4776115119457245},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4647499918937683},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41644641757011414},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.41349658370018005},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.4129725992679596},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.408551424741745},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.343824177980423},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3118894100189209},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22430625557899475},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.104522705078125},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","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":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1007/s10822-009-9277-0","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-009-9277-0","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:19548090","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19548090","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":"Journal of computer-aided molecular design","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities","score":0.6899999976158142}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1483008427","https://openalex.org/W1970692848","https://openalex.org/W1982547008","https://openalex.org/W2014474863","https://openalex.org/W2023790301","https://openalex.org/W2024949451","https://openalex.org/W2026956259","https://openalex.org/W2029667189","https://openalex.org/W2053803268","https://openalex.org/W2054980108","https://openalex.org/W2059067075","https://openalex.org/W2077180051","https://openalex.org/W2077847478","https://openalex.org/W2084998761","https://openalex.org/W2085277871","https://openalex.org/W2086358466","https://openalex.org/W2089848513","https://openalex.org/W2098084175","https://openalex.org/W2100262865","https://openalex.org/W2103150692","https://openalex.org/W2115138247","https://openalex.org/W2121704271","https://openalex.org/W2126350253","https://openalex.org/W2133865862","https://openalex.org/W2139608682","https://openalex.org/W2149138213","https://openalex.org/W2157236640","https://openalex.org/W2160216877","https://openalex.org/W4246975107"],"related_works":["https://openalex.org/W2170471837","https://openalex.org/W2593264178","https://openalex.org/W158041880","https://openalex.org/W2384478968","https://openalex.org/W2078866107","https://openalex.org/W2181530468","https://openalex.org/W1600613454","https://openalex.org/W1966388405","https://openalex.org/W2005785288","https://openalex.org/W3168591324"],"abstract_inverted_index":null,"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}