{"id":"https://openalex.org/W2564815219","doi":"https://doi.org/10.1109/iccabs.2016.7802777","title":"Assessing how multiple mutations affect protein stability using rigid cluster size distributions","display_name":"Assessing how multiple mutations affect protein stability using rigid cluster size distributions","publication_year":2016,"publication_date":"2016-10-01","ids":{"openalex":"https://openalex.org/W2564815219","doi":"https://doi.org/10.1109/iccabs.2016.7802777","mag":"2564815219"},"language":"en","primary_location":{"id":"doi:10.1109/iccabs.2016.7802777","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2016.7802777","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","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/A5031412856","display_name":"Erik Andersson","orcid":"https://orcid.org/0000-0003-0088-8719"},"institutions":[{"id":"https://openalex.org/I52669646","display_name":"Western Washington University","ror":"https://ror.org/05wn7r715","country_code":"US","type":"education","lineage":["https://openalex.org/I52669646"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Erik Andersson","raw_affiliation_strings":["Western Washington University, Bellingham, WA"],"affiliations":[{"raw_affiliation_string":"Western Washington University, Bellingham, WA","institution_ids":["https://openalex.org/I52669646"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076797883","display_name":"Rebecca Hsieh","orcid":null},"institutions":[{"id":"https://openalex.org/I52669646","display_name":"Western Washington University","ror":"https://ror.org/05wn7r715","country_code":"US","type":"education","lineage":["https://openalex.org/I52669646"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rebecca Hsieh","raw_affiliation_strings":["Western Washington University, Bellingham, WA"],"affiliations":[{"raw_affiliation_string":"Western Washington University, Bellingham, WA","institution_ids":["https://openalex.org/I52669646"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073677323","display_name":"Howard Szeto","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Howard Szeto","raw_affiliation_strings":["University Massachusetts Boston, Boston, MA"],"affiliations":[{"raw_affiliation_string":"University Massachusetts Boston, Boston, MA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049482670","display_name":"Roshanak Farhoodi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Roshanak Farhoodi","raw_affiliation_strings":["University Massachusetts Boston, Boston, MA"],"affiliations":[{"raw_affiliation_string":"University Massachusetts Boston, Boston, MA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053405483","display_name":"Nurit Haspel","orcid":"https://orcid.org/0000-0003-4810-379X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nurit Haspel","raw_affiliation_strings":["University Massachusetts Boston, Boston, MA"],"affiliations":[{"raw_affiliation_string":"University Massachusetts Boston, Boston, MA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046109728","display_name":"Filip Jagodzinski","orcid":"https://orcid.org/0000-0001-7783-2241"},"institutions":[{"id":"https://openalex.org/I52669646","display_name":"Western Washington University","ror":"https://ror.org/05wn7r715","country_code":"US","type":"education","lineage":["https://openalex.org/I52669646"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Filip Jagodzinski","raw_affiliation_strings":["Western Washington University, Bellingham, WA"],"affiliations":[{"raw_affiliation_string":"Western Washington University, Bellingham, WA","institution_ids":["https://openalex.org/I52669646"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5031412856"],"corresponding_institution_ids":["https://openalex.org/I52669646"],"apc_list":null,"apc_paid":null,"fwci":0.8336,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.76528921,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"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":0.9995999932289124,"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":0.9995999932289124,"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":0.9961000084877014,"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":0.9898999929428101,"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/in-silico","display_name":"In silico","score":0.6723699569702148},{"id":"https://openalex.org/keywords/rigidity","display_name":"Rigidity (electromagnetism)","score":0.5338783264160156},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5184740424156189},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.504292368888855},{"id":"https://openalex.org/keywords/mutant","display_name":"Mutant","score":0.5038549304008484},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.4930109679698944},{"id":"https://openalex.org/keywords/cluster","display_name":"Cluster (spacecraft)","score":0.4558907151222229},{"id":"https://openalex.org/keywords/random-forest","display_name":"Random forest","score":0.44420143961906433},{"id":"https://openalex.org/keywords/cluster-size","display_name":"Cluster size","score":0.4435107409954071},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3692750930786133},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.34646961092948914},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3007407784461975},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28417253494262695},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.27808254957199097},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23874080181121826},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.17721021175384521},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.1768738031387329},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11166176199913025},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10945376753807068},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.09325021505355835}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.6723699569702148},{"id":"https://openalex.org/C160343418","wikidata":"https://www.wikidata.org/wiki/Q185256","display_name":"Rigidity (electromagnetism)","level":2,"score":0.5338783264160156},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5184740424156189},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.504292368888855},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.5038549304008484},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.4930109679698944},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.4558907151222229},{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.44420143961906433},{"id":"https://openalex.org/C3017540586","wikidata":"https://www.wikidata.org/wiki/Q612728","display_name":"Cluster size","level":3,"score":0.4435107409954071},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3692750930786133},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34646961092948914},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3007407784461975},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28417253494262695},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.27808254957199097},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23874080181121826},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.17721021175384521},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.1768738031387329},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11166176199913025},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10945376753807068},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.09325021505355835},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/iccabs.2016.7802777","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2016.7802777","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5099999904632568,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W34482235","https://openalex.org/W1537349924","https://openalex.org/W1574312817","https://openalex.org/W1968755024","https://openalex.org/W1970294718","https://openalex.org/W1981428525","https://openalex.org/W1994337497","https://openalex.org/W2019574765","https://openalex.org/W2024281488","https://openalex.org/W2025786614","https://openalex.org/W2038639437","https://openalex.org/W2039388179","https://openalex.org/W2054243594","https://openalex.org/W2060435263","https://openalex.org/W2073758233","https://openalex.org/W2092387745","https://openalex.org/W2093547815","https://openalex.org/W2099672241","https://openalex.org/W2101234009","https://openalex.org/W2116274509","https://openalex.org/W2121519777","https://openalex.org/W2125677968","https://openalex.org/W2130479394","https://openalex.org/W2132540199","https://openalex.org/W2136513422","https://openalex.org/W2140227530","https://openalex.org/W2145644903","https://openalex.org/W2149580316","https://openalex.org/W2153635508","https://openalex.org/W2161162779","https://openalex.org/W2168129450","https://openalex.org/W2170342322","https://openalex.org/W2911964244","https://openalex.org/W6674788503"],"related_works":["https://openalex.org/W2900532910","https://openalex.org/W2513589746","https://openalex.org/W2003194288","https://openalex.org/W4280494160","https://openalex.org/W2213189664","https://openalex.org/W2153919606","https://openalex.org/W2048867280","https://openalex.org/W4385346653","https://openalex.org/W1494462539","https://openalex.org/W3111875760"],"abstract_inverted_index":{"Predicting":[0],"how":[1],"amino":[2,84,119],"acid":[3,85,120],"substitutions":[4],"affect":[5],"the":[6,20,34,47,62,96,103,115,118,125,139,151,161,186,193],"stability":[7,187],"of":[8,22,36,49,64,98,102,117,127,141,153,163,188,196],"a":[9,57,70,89,168,189,197],"protein":[10,24],"has":[11],"relevance":[12],"to":[13,33,45,94,113,159,179,185],"drug":[14],"design":[15],"and":[16,32,66,106],"may":[17],"help":[18],"elucidate":[19],"mechanisms":[21],"disease-causing":[23],"variants.":[25],"Unfortunately,":[26],"wet-lab":[27],"experiments":[28],"are":[29,40,183],"time":[30],"intensive,":[31],"best":[35],"our":[37,132,142],"knowledge":[38],"there":[39],"no":[41],"efficient":[42],"computational":[43,143],"techniques":[44],"asses":[46],"effect":[48,116],"multiple":[50,67,83,128,200],"mutations.":[51],"In":[52],"this":[53],"work":[54],"we":[55,110,165],"present":[56,167],"new":[58],"approach":[59,93,144,173],"for":[60,130],"inferring":[61],"effects":[63,126,162,195],"single":[65,81,198],"mutations":[68,129,201],"on":[69,176],"protein's":[71],"structure.":[72],"Our":[73],"rMutant":[74],"algorithm":[75],"generates":[76],"in":[77],"silico":[78],"mutants":[79],"with":[80,202],"or":[82,199],"substitutions.":[86,121],"We":[87,122,137,191],"use":[88],"graph-theoretic":[90],"rigidity":[91,177],"analysis":[92],"compute":[95],"distributions":[97,158],"rigid":[99,155],"cluster":[100,156],"sizes":[101],"wild":[104],"type":[105],"mutant":[107],"structures":[108],"which":[109,131,181],"then":[111],"analyze":[112],"infer":[114,160],"successfully":[123],"predict":[124,180,192],"previous":[133],"methods":[134],"were":[135],"unsuccessful.":[136],"validate":[138],"predictions":[140],"against":[145],"experimental":[146],"\u0394\u0394G":[147],"data.":[148],"To":[149],"demonstrate":[150],"utility":[152],"using":[154],"size":[157],"mutations,":[164],"also":[166],"Random":[169],"Forest":[170],"Machine":[171],"Learning":[172],"that":[174],"relies":[175],"data":[178],"residues":[182],"critical":[184],"protein.":[190],"destabilizing":[194],"over":[203],"86%":[204],"accuracy.":[205]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
