{"id":"https://openalex.org/W2093265673","doi":"https://doi.org/10.1186/1471-2105-11-s10-o4","title":"Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease","display_name":"Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease","publication_year":2010,"publication_date":"2010-12-01","ids":{"openalex":"https://openalex.org/W2093265673","doi":"https://doi.org/10.1186/1471-2105-11-s10-o4","mag":"2093265673"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-s10-o4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s10-o4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-11-S10-O4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-11-S10-O4","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064429259","display_name":"Fuxiao Xin","orcid":null},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Fuxiao Xin","raw_affiliation_strings":["School of Informatics and Computing, Indiana University, Bloomington, Indiana, 47408, USA","School of Informatics and Computing, Indiana University Bloomington, USA"],"affiliations":[{"raw_affiliation_string":"School of Informatics and Computing, Indiana University, Bloomington, Indiana, 47408, USA","institution_ids":["https://openalex.org/I4210119109"]},{"raw_affiliation_string":"School of Informatics and Computing, Indiana University Bloomington, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075913896","display_name":"Steven Myers","orcid":"https://orcid.org/0000-0001-8885-8770"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven Myers","raw_affiliation_strings":["School of Informatics and Computing, Indiana University, Bloomington, Indiana, 47408, USA","School of Informatics and Computing, Indiana University Bloomington, USA"],"affiliations":[{"raw_affiliation_string":"School of Informatics and Computing, Indiana University, Bloomington, Indiana, 47408, USA","institution_ids":["https://openalex.org/I4210119109"]},{"raw_affiliation_string":"School of Informatics and Computing, Indiana University Bloomington, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048125824","display_name":"Yong Fuga Li","orcid":"https://orcid.org/0000-0003-2116-3223"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yong Fuga Li","raw_affiliation_strings":["School of Informatics and Computing, Indiana University, Bloomington, Indiana, 47408, USA","School of Informatics and Computing, Indiana University Bloomington, USA"],"affiliations":[{"raw_affiliation_string":"School of Informatics and Computing, Indiana University, Bloomington, Indiana, 47408, USA","institution_ids":["https://openalex.org/I4210119109"]},{"raw_affiliation_string":"School of Informatics and Computing, Indiana University Bloomington, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042443600","display_name":"D.N. Cooper","orcid":"https://orcid.org/0000-0002-8943-8484"},"institutions":[{"id":"https://openalex.org/I79510175","display_name":"Cardiff University","ror":"https://ror.org/03kk7td41","country_code":"GB","type":"education","lineage":["https://openalex.org/I79510175"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"David N Cooper","raw_affiliation_strings":["Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK","Institute of Medical Genetics; School of Medicine; Cardiff University; Cardiff UK"],"affiliations":[{"raw_affiliation_string":"Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK","institution_ids":["https://openalex.org/I79510175"]},{"raw_affiliation_string":"Institute of Medical Genetics; School of Medicine; Cardiff University; Cardiff UK","institution_ids":["https://openalex.org/I79510175"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066000877","display_name":"Sean D. Mooney","orcid":"https://orcid.org/0000-0003-2654-0833"},"institutions":[{"id":"https://openalex.org/I1337826666","display_name":"Buck Institute for Research on Aging","ror":"https://ror.org/050sv4x28","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1337826666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sean D Mooney","raw_affiliation_strings":["Buck Institute for Age Research, Novato, California, 94945, USA","Buck Institute for Age Research, Novato, USA"],"affiliations":[{"raw_affiliation_string":"Buck Institute for Age Research, Novato, California, 94945, USA","institution_ids":["https://openalex.org/I1337826666"]},{"raw_affiliation_string":"Buck Institute for Age Research, Novato, USA","institution_ids":["https://openalex.org/I1337826666"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051324698","display_name":"Predrag Radivojac","orcid":"https://orcid.org/0000-0002-6769-0793"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Predrag Radivojac","raw_affiliation_strings":["School of Informatics and Computing, Indiana University, Bloomington, Indiana, 47408, USA","School of Informatics and Computing, Indiana University Bloomington, USA"],"affiliations":[{"raw_affiliation_string":"School of Informatics and Computing, Indiana University, Bloomington, Indiana, 47408, USA","institution_ids":["https://openalex.org/I4210119109"]},{"raw_affiliation_string":"School of Informatics and Computing, Indiana University Bloomington, USA","institution_ids":["https://openalex.org/I4210119109"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5064429259"],"corresponding_institution_ids":["https://openalex.org/I4210119109"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.5287,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.65844616,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"11","issue":"S10","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":0.9988999962806702,"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":0.9988999962806702,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9977999925613403,"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":0.9976999759674072,"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/computational-biology","display_name":"Computational biology","score":0.6038736701011658},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5339784622192383},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.517906129360199},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4348601698875427},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.43450137972831726},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.36860525608062744},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19083857536315918},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.18641826510429382},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1080358624458313},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.07712674140930176}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6038736701011658},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5339784622192383},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.517906129360199},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4348601698875427},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.43450137972831726},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.36860525608062744},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19083857536315918},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.18641826510429382},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1080358624458313},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.07712674140930176}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1186/1471-2105-11-s10-o4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s10-o4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-11-S10-O4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-s10-o4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s10-o4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-11-S10-O4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.6299999952316284}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2093265673.pdf","grobid_xml":"https://content.openalex.org/works/W2093265673.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W2139099905","https://openalex.org/W2154333184","https://openalex.org/W2154927232"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W1641042124","https://openalex.org/W2013243191","https://openalex.org/W2151865869","https://openalex.org/W2117258802","https://openalex.org/W2051339581","https://openalex.org/W4234157524"],"abstract_inverted_index":{"Motivation:":[0],"Enzyme":[1],"catalysis":[2],"is":[3,198,229],"involved":[4,216],"in":[5,18,66,112,190,217],"numerous":[6],"biological":[7],"processes":[8],"and":[9,39,73,98,126,139,221],"the":[10,34,40,51,58,67,76,88,131,135,169,185,192,203,226],"disruption":[11,204],"of":[12,25,36,42,54,69,79,90,107,134,142,173,188,196,205],"enzymatic":[13],"activity":[14],"has":[15,57],"been":[16],"implicated":[17],"human":[19,218],"disease.":[20],"Despite":[21],"this,":[22],"various":[23],"aspects":[24],"catalytic":[26,43,55,63,91,143,174],"reactions":[27],"are":[28,214,236],"not":[29,199],"completely":[30],"understood,":[31],"such":[32],"as":[33],"mechanics":[35],"reaction":[37],"chemistry":[38],"geometry":[41],"residues":[44,56,92],"within":[45],"active":[46],"sites.":[47],"As":[48],"a":[49,83,180],"result,":[50],"computational":[52],"prediction":[53,89],"potential":[59],"to":[60,151,165,183],"identify":[61,152],"novel":[62],"pockets,":[64],"aid":[65],"design":[68],"more":[70],"efficient":[71],"enzymes":[72],"also":[74,127],"predict":[75],"molecular":[77,160,186],"basis":[78,187],"disease.\r\n\r\nResults:":[80],"We":[81,115],"propose":[82],"new":[84,147],"kernel-based":[85],"algorithm":[86,120,148],"for":[87,225],"based":[93],"on":[94],"protein":[95,113,206],"sequence,":[96],"structure":[97],"evolutionary":[99,140],"information.":[100],"The":[101,146],"method":[102],"relies":[103],"upon":[104],"explicit":[105],"modeling":[106],"similarity":[108],"between":[109],"residue-centered":[110],"neighborhoods":[111],"structures.":[114],"present":[116],"evidence":[117],"that":[118,211],"this":[119],"evaluates":[121],"favorably":[122],"against":[123],"established":[124],"approaches,":[125],"provides":[128],"insights":[129],"into":[130],"relative":[132],"importance":[133],"geometry,":[136],"physicochemical":[137],"properties":[138],"conservation":[141],"residue":[144],"activity.":[145],"was":[149],"used":[150],"known":[153],"mutations":[154],"associated":[155],"with":[156],"inherited":[157,219],"disease":[158,189],"whose":[159],"mechanism":[161],"might":[162],"be":[163],"predicted":[164],"operate":[166],"specifically":[167],"though":[168],"loss":[170,193],"or":[171,194],"gain":[172,195],"residues.":[175],"It":[176],"should,":[177],"therefore,":[178],"provide":[179],"viable":[181],"approach":[182],"identifying":[184],"which":[191],"function":[197],"caused":[200],"solely":[201],"by":[202],"stability.":[207],"Our":[208],"analysis":[209],"suggests":[210],"both":[212],"mechanisms":[213],"actively":[215],"disease.\r\n\r\nAvailability":[220],"Implementation:":[222],"Source":[223],"code":[224],"structural":[227],"kernel":[228],"available":[230,237],"at":[231,238],"www.informatics.indiana.edu/predrag/\r\n\r\nContact:":[232],"[email\u00a0protected]\r\n\r\nSupplementary":[233],"information:Supplementary":[234],"data":[235],"Bioinformatics":[239],"online.":[240]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
