{"id":"https://openalex.org/W2769187995","doi":"https://doi.org/10.1109/iccabs.2017.8114301","title":"Efficient pebble game algorithms engineered for protein rigidity applications","display_name":"Efficient pebble game algorithms engineered for protein rigidity applications","publication_year":2017,"publication_date":"2017-10-01","ids":{"openalex":"https://openalex.org/W2769187995","doi":"https://doi.org/10.1109/iccabs.2017.8114301","mag":"2769187995"},"language":"en","primary_location":{"id":"doi:10.1109/iccabs.2017.8114301","doi":"https://doi.org/10.1109/iccabs.2017.8114301","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2017.8114301","pdf_url":null,"source":{"id":"https://openalex.org/S4393918246","display_name":"IEEE International Conference on Computational Advances in Bio and Medical Sciences","issn_l":"2164-229X","issn":["2164-229X"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE 7th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"},"volume":null,"type":"conference-paper","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/A5035332503","display_name":"Mojtaba Nouri Bygi","orcid":null,"observed_orcids":[]},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mojtaba Nouri Bygi","raw_affiliation_strings":["Department of Computer Science, Smith College Northampton, Massachusetts, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Smith College Northampton, Massachusetts, USA","institution_ids":["https://openalex.org/I202524275"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008565320","display_name":"Ileana Streinu","orcid":"https://orcid.org/0000-0003-2663-2615","observed_orcids":["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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ileana Streinu","raw_affiliation_strings":["Department of Computer Science, Smith College Northampton, Massachusetts, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Smith College Northampton, Massachusetts, USA","institution_ids":["https://openalex.org/I202524275"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I202524275"],"apc_list":null,"apc_paid":null,"fwci":1.0196,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.81380563,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9990000128746033,"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":0.9990000128746033,"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":0.00039999998989515007,"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/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-rigidity","display_name":"protein rigidity","score":0.8109999895095825},{"id":"https://openalex.org/keywords/protein-flexibility","display_name":"protein flexibility","score":0.878000020980835},{"id":"https://openalex.org/keywords/protein-unfolding","display_name":"protein unfolding","score":0.5839999914169312}],"concepts":[{"id":"https://openalex.org/C160343418","wikidata":"https://www.wikidata.org/wiki/Q185256","display_name":"Rigidity (electromagnetism)","level":2,"score":0.8050190210342407},{"id":"https://openalex.org/C155759531","wikidata":"https://www.wikidata.org/wiki/Q7625050","display_name":"Structural rigidity","level":2,"score":0.7260907888412476},{"id":"https://openalex.org/C2777760186","wikidata":"https://www.wikidata.org/wiki/Q14673","display_name":"Pebble","level":2,"score":0.6795337200164795},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6349092721939087},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.5903486609458923},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5159435868263245},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.38493406772613525},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.33167165517807007},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.17451602220535278},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.15090897679328918},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14970508217811584},{"id":"https://openalex.org/C114793014","wikidata":"https://www.wikidata.org/wiki/Q52109","display_name":"Geomorphology","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/iccabs.2017.8114301","doi":"https://doi.org/10.1109/iccabs.2017.8114301","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2017.8114301","pdf_url":null,"source":{"id":"https://openalex.org/S4393918246","display_name":"IEEE International Conference on Computational Advances in Bio and Medical Sciences","issn_l":"2164-229X","issn":["2164-229X"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE 7th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"},{"id":"pmh:oai:scholarworks.smith.edu:csc_facpubs-1241","doi":null,"is_oa":false,"landing_page_url":"https://scholarworks.smith.edu/csc_facpubs/240","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,"listed_in":[],"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-1293","doi":null,"is_oa":false,"landing_page_url":"https://scholarworks.smith.edu/csc_facpubs/292","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,"listed_in":[],"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":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W117865858","https://openalex.org/W754150909","https://openalex.org/W1969231606","https://openalex.org/W1994337497","https://openalex.org/W1999823897","https://openalex.org/W2045768640","https://openalex.org/W2069308938","https://openalex.org/W2093547815","https://openalex.org/W2100284567","https://openalex.org/W2122599408","https://openalex.org/W2137496915","https://openalex.org/W2144646547","https://openalex.org/W2155812479","https://openalex.org/W2164073568","https://openalex.org/W2282508912","https://openalex.org/W2493898829","https://openalex.org/W2580672700"],"related_works":["https://openalex.org/W2774349728","https://openalex.org/W4415620628","https://openalex.org/W2589648848","https://openalex.org/W2111876575","https://openalex.org/W2057618548","https://openalex.org/W2102169545","https://openalex.org/W2282508912","https://openalex.org/W7100806380","https://openalex.org/W1592979571","https://openalex.org/W2167279640"],"abstract_inverted_index":{"Pebble":[0],"game":[1,71],"rigidity":[2,10],"analysis":[3],"is":[4],"an":[5,36],"efficient":[6],"method":[7],"for":[8],"extracting":[9],"and":[11,46,55],"flexibility":[12,45],"information":[13],"of":[14,63,78],"biomolecules":[15],"without":[16],"performing":[17],"costly":[18],"molecular":[19],"dynamics":[20],"simulations.":[21],"The":[22],"standard":[23],"algorithm":[24],"works":[25],"on":[26],"a":[27,31,53],"multi-graph":[28],"associated":[29],"to":[30,60],"mechanical":[32],"model":[33],"constructed":[34],"from":[35],"arbitrary":[37],"atom-bond":[38],"network.":[39],"Motivated":[40],"by":[41],"large":[42],"scale":[43],"protein":[44],"simulated":[47],"unfolding":[48],"applications,":[49],"we":[50],"have":[51],"developed":[52],"faster":[54],"more":[56],"robust":[57],"variation":[58],"tailored":[59],"the":[61,75],"specificities":[62],"bio-polymers.":[64],"We":[65],"describe":[66],"this":[67],"new":[68,76],"phased":[69],"pebble":[70],"as":[72],"implemented":[73],"in":[74],"version":[77],"our":[79],"software":[80],"Kinari-2.":[81]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-11-01T11:40:01.658920","created_date":"2017-12-04T00:00:00"}