{"id":"https://openalex.org/W2044725845","doi":"https://doi.org/10.1109/iccabs.2012.6182632","title":"Towards accurate modeling for protein rigidity analysis","display_name":"Towards accurate modeling for protein rigidity analysis","publication_year":2012,"publication_date":"2012-02-01","ids":{"openalex":"https://openalex.org/W2044725845","doi":"https://doi.org/10.1109/iccabs.2012.6182632","mag":"2044725845"},"language":"en","primary_location":{"id":"doi:10.1109/iccabs.2012.6182632","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2012.6182632","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 2nd 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/A5029772260","display_name":"Naomi K. Fox","orcid":"https://orcid.org/0000-0003-2828-858X"},"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":"Naomi Fox","raw_affiliation_strings":["Department of Computer Science, University of Massachusetts, Amherst, MA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, 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/I202524275","display_name":"Smith College","ror":"https://ror.org/0497crr92","country_code":"US","type":"education","lineage":["https://openalex.org/I202524275"]},{"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":"Ileana Streinu","raw_affiliation_strings":["Department of Computer Science, Smith College, Northampton, MA, USA","University of Massachusetts, 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":"University of Massachusetts, Amherst, MA, USA","institution_ids":["https://openalex.org/I24603500"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5029772260"],"corresponding_institution_ids":["https://openalex.org/I24603500"],"apc_list":null,"apc_paid":null,"fwci":0.4391,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.60251437,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"2","issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9998000264167786,"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/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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9789000153541565,"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/cutoff","display_name":"Cutoff","score":0.6961137056350708},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5834564566612244},{"id":"https://openalex.org/keywords/rigidity","display_name":"Rigidity (electromagnetism)","score":0.5475344657897949},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5443801283836365},{"id":"https://openalex.org/keywords/hydrogen-bond","display_name":"Hydrogen bond","score":0.4484250843524933},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4016703963279724},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38052088022232056},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2716670334339142},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.12187322974205017},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.11446380615234375}],"concepts":[{"id":"https://openalex.org/C2778217198","wikidata":"https://www.wikidata.org/wiki/Q556977","display_name":"Cutoff","level":2,"score":0.6961137056350708},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5834564566612244},{"id":"https://openalex.org/C160343418","wikidata":"https://www.wikidata.org/wiki/Q185256","display_name":"Rigidity (electromagnetism)","level":2,"score":0.5475344657897949},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5443801283836365},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.4484250843524933},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4016703963279724},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38052088022232056},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2716670334339142},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.12187322974205017},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.11446380615234375},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"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/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/iccabs.2012.6182632","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2012.6182632","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"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"},{"id":"https://openalex.org/F4320332172","display_name":"Directorate for Mathematical and Physical Sciences","ror":"https://ror.org/029b7h395"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1994337497","https://openalex.org/W2019004327","https://openalex.org/W2045768640","https://openalex.org/W2069308938","https://openalex.org/W2082653344","https://openalex.org/W2093547815","https://openalex.org/W2102713398","https://openalex.org/W2103885137","https://openalex.org/W2113227740","https://openalex.org/W2121403868","https://openalex.org/W2146316980","https://openalex.org/W2164073568","https://openalex.org/W2168989513","https://openalex.org/W2953288379"],"related_works":["https://openalex.org/W4285208670","https://openalex.org/W3092388660","https://openalex.org/W1778838665","https://openalex.org/W2378211422","https://openalex.org/W2328322229","https://openalex.org/W4321353415","https://openalex.org/W2745001401","https://openalex.org/W3175879137","https://openalex.org/W2130974462","https://openalex.org/W3204534828"],"abstract_inverted_index":{"We":[0,72,90,184],"evaluate":[1],"the":[2,5,25,30,42,50,54,69,75,76,85,106,119,127,134,139,150,158,162,168,186,189],"performance":[3],"of":[4,19,68,109,149,181,188],"modeling":[6,95,172],"in":[7,82],"KINARI,":[8],"our":[9,170],"pebble-game":[10],"rigidity":[11,83],"analysis":[12],"system,":[13],"on":[14,65,74,196],"a":[15,37,62,93,115,165],"benchmark":[16],"data":[17],"set":[18],"32":[20],"PDB":[21],"files":[22],"used":[23,60,79,141],"by":[24],"Gerstein":[26],"Lab":[27],"to":[28,157],"validate":[29],"RigidFinder":[31],"algorithm.":[32],"For":[33,118,147,161],"this":[34],"we":[35],"use":[36],"novel":[38],"evaluation":[39],"method,":[40],"called":[41],"cluster":[43,190],"decomposition":[44,191],"score.":[45],"This":[46],"is":[47,59,142],"adapted":[48],"from":[49,53],"B-cubed":[51],"score":[52,64,192],"information":[55],"retrieval":[56],"literature,":[57],"which":[58],"as":[61],"comparative":[63],"two":[66],"clusterings":[67],"same":[70],"data.":[71],"focus":[73],"most":[77,148],"extensively":[78],"tuning":[80],"parameter":[81],"analysis,":[84],"hydrogen":[86,98,154],"bond":[87],"energy":[88],"cutoff.":[89],"also":[91],"propose":[92],"new":[94,171],"methodology":[96,173],"for":[97,144,178],"bonds,":[99],"where":[100,164],"those":[101],"with":[102,114,193],"energies":[103],"lower":[104],"than":[105,133],"cutoff,":[107],"instead":[108],"being":[110],"discarded,":[111],"are":[112],"modeled":[113],"weaker":[116],"constraint.":[117],"5":[120],"largest":[121],"proteins":[122,151],"(501":[123],"residues":[124],"or":[125,175],"more),":[126],"KINARI":[128],"decompositions":[129],"scored":[130],"significantly":[131],"better":[132],"crude":[135],"baseline,":[136],"indicating":[137],"that":[138],"parameterization":[140],"reliable":[143],"larger":[145],"proteins.":[146],"including":[152],"all":[153],"bonds":[155],"leads":[156],"best":[159],"scores.":[160],"others,":[163],"cutoff":[166],"improved":[167,176],"score,":[169],"matched":[174],"results":[177],"9":[179],"out":[180],"10":[182],"PDBs.":[183],"investigate":[185],"sensitivity":[187],"case":[194],"studies":[195],"pyruvate":[197],"phosphate":[198],"dikinase":[199],"and":[200],"phosphotransferase.":[201]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
