{"id":"https://openalex.org/W2058177295","doi":"https://doi.org/10.1109/bibmw.2011.6112410","title":"Using rigidity analysis to probe mutation-induced structural changes in proteins","display_name":"Using rigidity analysis to probe mutation-induced structural changes in proteins","publication_year":2011,"publication_date":"2011-11-01","ids":{"openalex":"https://openalex.org/W2058177295","doi":"https://doi.org/10.1109/bibmw.2011.6112410","mag":"2058177295"},"language":"en","primary_location":{"id":"doi:10.1109/bibmw.2011.6112410","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibmw.2011.6112410","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5044591351","display_name":"F. Jagodzinski","orcid":null},"institutions":[{"id":"https://openalex.org/I24603500","display_name":"University of Massachusetts Amherst","ror":"https://ror.org/0072zz521","country_code":"US","type":"education","lineage":["https://openalex.org/I24603500"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"F. Jagodzinski","raw_affiliation_strings":["Department of Computer Science, University of Massachusetts, Amherst, Amherst, MA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Massachusetts, Amherst, Amherst, MA, USA","institution_ids":["https://openalex.org/I24603500"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004556923","display_name":"Jeanne A. Hardy","orcid":"https://orcid.org/0000-0002-3406-7997"},"institutions":[{"id":"https://openalex.org/I24603500","display_name":"University of Massachusetts Amherst","ror":"https://ror.org/0072zz521","country_code":"US","type":"education","lineage":["https://openalex.org/I24603500"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. Hardy","raw_affiliation_strings":["Department of Chemistry, University of Massachusetts, Amherst, MA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Massachusetts, Amherst, MA, USA","institution_ids":["https://openalex.org/I24603500"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008565320","display_name":"Ileana Streinu","orcid":"https://orcid.org/0000-0003-2663-2615"},"institutions":[{"id":"https://openalex.org/I24603500","display_name":"University of Massachusetts Amherst","ror":"https://ror.org/0072zz521","country_code":"US","type":"education","lineage":["https://openalex.org/I24603500"]},{"id":"https://openalex.org/I202524275","display_name":"Smith College","ror":"https://ror.org/0497crr92","country_code":"US","type":"education","lineage":["https://openalex.org/I202524275"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"I. Streinu","raw_affiliation_strings":["Department of Computer Science, Smith College, Northampton, MA, USA","Department of Computer Science, University of Massachusetts, Amherst, Amherst, MA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Smith College, Northampton, MA, USA","institution_ids":["https://openalex.org/I202524275"]},{"raw_affiliation_string":"Department of Computer Science, University of Massachusetts, Amherst, Amherst, MA, USA","institution_ids":["https://openalex.org/I24603500"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5044591351"],"corresponding_institution_ids":["https://openalex.org/I24603500"],"apc_list":null,"apc_paid":null,"fwci":0.1334,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.53173779,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"253","issue":null,"first_page":"432","last_page":"437"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9922000169754028,"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":0.9922000169754028,"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/T10404","display_name":"Enzyme Catalysis and Immobilization","score":0.9825000166893005,"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/T10839","display_name":"Pancreatic function and diabetes","score":0.9819999933242798,"subfield":{"id":"https://openalex.org/subfields/2746","display_name":"Surgery"},"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/mutagen","display_name":"Mutagen","score":0.7665108442306519},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.6805799007415771},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.5692229866981506},{"id":"https://openalex.org/keywords/protein-engineering","display_name":"Protein engineering","score":0.5271339416503906},{"id":"https://openalex.org/keywords/mutant","display_name":"Mutant","score":0.5219684839248657},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.49652916193008423},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.45007139444351196},{"id":"https://openalex.org/keywords/mutant-protein","display_name":"Mutant protein","score":0.43193820118904114},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4191647171974182},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3722843527793884},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3620437979698181},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35949480533599854},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.27984464168548584},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.19237351417541504},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11732211709022522}],"concepts":[{"id":"https://openalex.org/C2776639595","wikidata":"https://www.wikidata.org/wiki/Q221696","display_name":"Mutagen","level":3,"score":0.7665108442306519},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.6805799007415771},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.5692229866981506},{"id":"https://openalex.org/C147816474","wikidata":"https://www.wikidata.org/wiki/Q169525","display_name":"Protein engineering","level":3,"score":0.5271339416503906},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.5219684839248657},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.49652916193008423},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.45007139444351196},{"id":"https://openalex.org/C2779926675","wikidata":"https://www.wikidata.org/wiki/Q6943700","display_name":"Mutant protein","level":4,"score":0.43193820118904114},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4191647171974182},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3722843527793884},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3620437979698181},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35949480533599854},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.27984464168548584},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.19237351417541504},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11732211709022522},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/bibmw.2011.6112410","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibmw.2011.6112410","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)","raw_type":"proceedings-article"},{"id":"pmh:oai:scholarworks.smith.edu:csc_facpubs-1276","is_oa":false,"landing_page_url":"https://scholarworks.smith.edu/csc_facpubs/275","pdf_url":null,"source":{"id":"https://openalex.org/S4377196392","display_name":"Smith ScholarWorks (Smith College)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I202524275","host_organization_name":"Smith College","host_organization_lineage":["https://openalex.org/I202524275"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computer Science: Faculty Publications","raw_type":"text"},{"id":"pmh:oai:scholarworks.smith.edu:csc_facpubs-1328","is_oa":false,"landing_page_url":"https://scholarworks.smith.edu/cgi/viewcontent.cgi?article=1328&context=csc_facpubs","pdf_url":null,"source":{"id":"https://openalex.org/S4377196392","display_name":"Smith ScholarWorks (Smith College)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I202524275","host_organization_name":"Smith College","host_organization_lineage":["https://openalex.org/I202524275"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computer Science: Faculty Publications","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.5799999833106995}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332180","display_name":"Defense Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1594663644","https://openalex.org/W1691290619","https://openalex.org/W1981428525","https://openalex.org/W1994334416","https://openalex.org/W1994337497","https://openalex.org/W2004360551","https://openalex.org/W2019574765","https://openalex.org/W2031311803","https://openalex.org/W2045768640","https://openalex.org/W2054243594","https://openalex.org/W2057400263","https://openalex.org/W2065843068","https://openalex.org/W2067130595","https://openalex.org/W2069297570","https://openalex.org/W2069308938","https://openalex.org/W2071770954","https://openalex.org/W2075481658","https://openalex.org/W2100284567","https://openalex.org/W2101481219","https://openalex.org/W2115592403","https://openalex.org/W2116173437","https://openalex.org/W2116274509","https://openalex.org/W2139834426","https://openalex.org/W2160185798","https://openalex.org/W2166149166","https://openalex.org/W4237172632"],"related_works":["https://openalex.org/W2912862995","https://openalex.org/W3129816939","https://openalex.org/W2101501829","https://openalex.org/W1828927697","https://openalex.org/W2985427592","https://openalex.org/W2003194288","https://openalex.org/W2185064957","https://openalex.org/W2038715930","https://openalex.org/W2071141854","https://openalex.org/W2740093802"],"abstract_inverted_index":{"Predicting":[0],"how":[1],"a":[2,11,15,36,81,84,116,121],"single":[3],"amino":[4,86,125],"acid":[5,87,126],"substitution":[6],"affects":[7],"the":[8,49,60,113],"stability":[9,118,135],"of":[10,29,59,62,123],"protein":[12,31,46,82],"structure":[13],"is":[14,75,138],"fundamental":[16],"task":[17],"in":[18,41,71,112,115],"macromolecular":[19],"modeling.":[20],"It":[21],"has":[22],"relevance":[23],"to":[24,69,79,96,103,120,127],"drug":[25],"design":[26],"and":[27,106],"understanding":[28],"disease-causing":[30],"variants.":[32],"We":[33],"present":[34],"KINARI-Mutagen,":[35],"web":[37],"server":[38],"for":[39],"performing":[40],"silico":[42],"mutation":[43,122],"experiments":[44],"on":[45],"structures":[47],"from":[48],"Protein":[50],"Data":[51],"Bank.":[52],"Our":[53],"rigidity-based":[54],"approach":[55],"permits":[56],"fast":[57],"evaluation":[58],"effects":[61],"mutations":[63],"that":[64,100,109],"may":[65],"not":[66,76],"be":[67,104,130],"easy":[68],"perform":[70],"vitro,":[72],"because":[73],"it":[74],"always":[77],"possible":[78],"express":[80],"with":[83],"specific":[85],"substitution.":[88],"In":[89],"two":[90],"case":[91],"studies":[92],"we":[93,107],"use":[94],"KINARI-Mutagen":[95,137],"identify":[97],"exposed":[98],"residues":[99],"are":[101],"known":[102],"conserved,":[105],"show":[108],"our":[110],"prediction":[111],"change":[114],"protein's":[117],"due":[119],"an":[124],"glycine":[128],"can":[129],"correlated":[131],"against":[132],"experimentally":[133],"derived":[134],"data.":[136],"available":[139],"at":[140],"http://kinari.cs.umass.edu.":[141]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
