{"id":"https://openalex.org/W2098084175","doi":"https://doi.org/10.1007/s10822-009-9273-4","title":"Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development","display_name":"Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development","publication_year":2009,"publication_date":"2009-06-19","ids":{"openalex":"https://openalex.org/W2098084175","doi":"https://doi.org/10.1007/s10822-009-9273-4","mag":"2098084175","pmid":"https://pubmed.ncbi.nlm.nih.gov/19543979"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-009-9273-4","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-009-9273-4","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/A5011567934","display_name":"Jan F. Prins","orcid":"https://orcid.org/0000-0003-0853-6099"},"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","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":"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","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":"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","University of North Carolina"],"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":"University of North Carolina","institution_ids":[]}]}],"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":1.0735,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.76438074,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"23","issue":"11","first_page":"773","last_page":"784"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"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":0.9997000098228455,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9990000128746033,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9984999895095825,"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/residue","display_name":"Residue (chemistry)","score":0.574669361114502},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5535927414894104},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4603092670440674},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4598245918750763},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.4577582776546478},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4114500880241394},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2804954946041107},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20401093363761902},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16094020009040833},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.14114248752593994},{"id":"https://openalex.org/keywords/botany","display_name":"Botany","score":0.10743927955627441}],"concepts":[{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.574669361114502},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5535927414894104},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4603092670440674},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4598245918750763},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.4577582776546478},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4114500880241394},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2804954946041107},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20401093363761902},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16094020009040833},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14114248752593994},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.10743927955627441},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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/s10822-009-9273-4","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-009-9273-4","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:19543979","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19543979","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/2","display_name":"Zero hunger","score":0.5}],"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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":93,"referenced_works":["https://openalex.org/W261268181","https://openalex.org/W1422803820","https://openalex.org/W1527927437","https://openalex.org/W1585607520","https://openalex.org/W1585634379","https://openalex.org/W1587558271","https://openalex.org/W1964640688","https://openalex.org/W1965907701","https://openalex.org/W1965910641","https://openalex.org/W1966388405","https://openalex.org/W1968682237","https://openalex.org/W1969230095","https://openalex.org/W1969738839","https://openalex.org/W1969867999","https://openalex.org/W1971155547","https://openalex.org/W1978098535","https://openalex.org/W1979147581","https://openalex.org/W1981575795","https://openalex.org/W1986154009","https://openalex.org/W1986969007","https://openalex.org/W1988044901","https://openalex.org/W1990453950","https://openalex.org/W1990495809","https://openalex.org/W1993731989","https://openalex.org/W1998931880","https://openalex.org/W1999319994","https://openalex.org/W2000377676","https://openalex.org/W2007978853","https://openalex.org/W2013882101","https://openalex.org/W2014926036","https://openalex.org/W2015147525","https://openalex.org/W2021954541","https://openalex.org/W2023790301","https://openalex.org/W2028697242","https://openalex.org/W2036696353","https://openalex.org/W2044667400","https://openalex.org/W2051895548","https://openalex.org/W2053803268","https://openalex.org/W2055345820","https://openalex.org/W2056477044","https://openalex.org/W2059067075","https://openalex.org/W2070436836","https://openalex.org/W2075986011","https://openalex.org/W2077847478","https://openalex.org/W2083654996","https://openalex.org/W2088534163","https://openalex.org/W2089593727","https://openalex.org/W2095298573","https://openalex.org/W2099013368","https://openalex.org/W2099485600","https://openalex.org/W2100320834","https://openalex.org/W2100494857","https://openalex.org/W2101220662","https://openalex.org/W2101252757","https://openalex.org/W2102122585","https://openalex.org/W2102333330","https://openalex.org/W2103150692","https://openalex.org/W2106694138","https://openalex.org/W2107327414","https://openalex.org/W2108067237","https://openalex.org/W2108302275","https://openalex.org/W2111973517","https://openalex.org/W2114197841","https://openalex.org/W2115138247","https://openalex.org/W2120138074","https://openalex.org/W2120564439","https://openalex.org/W2121166240","https://openalex.org/W2121704271","https://openalex.org/W2123070828","https://openalex.org/W2125725297","https://openalex.org/W2126359798","https://openalex.org/W2126991359","https://openalex.org/W2128996066","https://openalex.org/W2135338271","https://openalex.org/W2137991504","https://openalex.org/W2139608682","https://openalex.org/W2141032258","https://openalex.org/W2143011057","https://openalex.org/W2146940292","https://openalex.org/W2150444353","https://openalex.org/W2153153865","https://openalex.org/W2155367844","https://openalex.org/W2157236640","https://openalex.org/W2158714788","https://openalex.org/W2159400443","https://openalex.org/W2164750034","https://openalex.org/W2164886928","https://openalex.org/W2171004217","https://openalex.org/W2171602500","https://openalex.org/W2180389172","https://openalex.org/W2916193864","https://openalex.org/W3216627664","https://openalex.org/W6609551073"],"related_works":["https://openalex.org/W2032398765","https://openalex.org/W2898732673","https://openalex.org/W2391870038","https://openalex.org/W2053842772","https://openalex.org/W2410053581","https://openalex.org/W2383658677","https://openalex.org/W3123203398","https://openalex.org/W2084087543","https://openalex.org/W2354603059","https://openalex.org/W2610555415"],"abstract_inverted_index":null,"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}