{"id":"https://openalex.org/W4200336584","doi":"https://doi.org/10.3390/sym13122401","title":"CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins","display_name":"CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins","publication_year":2021,"publication_date":"2021-12-12","ids":{"openalex":"https://openalex.org/W4200336584","doi":"https://doi.org/10.3390/sym13122401"},"language":"en","primary_location":{"id":"doi:10.3390/sym13122401","is_oa":true,"landing_page_url":"https://doi.org/10.3390/sym13122401","pdf_url":"https://www.mdpi.com/2073-8994/13/12/2401/pdf?version=1639539847","source":{"id":"https://openalex.org/S190787756","display_name":"Symmetry","issn_l":"2073-8994","issn":["2073-8994"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Symmetry","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2073-8994/13/12/2401/pdf?version=1639539847","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040587306","display_name":"Alistair Turcan","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":"Alistair Turcan","raw_affiliation_strings":["Department of Computer Science, Western Washington University, Bellingham, WA 98225, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Western Washington University, Bellingham, WA 98225, USA","institution_ids":["https://openalex.org/I52669646"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084577541","display_name":"Anna Zivkovic","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":"Anna Zivkovic","raw_affiliation_strings":["Department of Computer Science, Western Washington University, Bellingham, WA 98225, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Western Washington University, Bellingham, WA 98225, USA","institution_ids":["https://openalex.org/I52669646"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044101172","display_name":"Dylan Thompson","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":"Dylan Thompson","raw_affiliation_strings":["Department of Computer Science, Western Washington University, Bellingham, WA 98225, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Western Washington University, Bellingham, WA 98225, USA","institution_ids":["https://openalex.org/I52669646"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026708392","display_name":"Lorraine Wong","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":"Lorraine Wong","raw_affiliation_strings":["Department of Computer Science, Western Washington University, Bellingham, WA 98225, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Western Washington University, Bellingham, WA 98225, USA","institution_ids":["https://openalex.org/I52669646"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102254930","display_name":"Lauren Johnson","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":"Lauren Johnson","raw_affiliation_strings":["Department of Computer Science, Western Washington University, Bellingham, WA 98225, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Western Washington University, Bellingham, WA 98225, USA","institution_ids":["https://openalex.org/I52669646"]}]},{"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":true,"raw_author_name":"Filip Jagodzinski","raw_affiliation_strings":["Department of Computer Science, Western Washington University, Bellingham, WA 98225, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Western Washington University, Bellingham, WA 98225, USA","institution_ids":["https://openalex.org/I52669646"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5046109728"],"corresponding_institution_ids":["https://openalex.org/I52669646"],"apc_list":{"value":2000,"currency":"CHF","value_usd":2165},"apc_paid":{"value":2000,"currency":"CHF","value_usd":2165},"fwci":0.1602,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.426015,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"13","issue":"12","first_page":"2401","last_page":"2401"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9980999827384949,"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":0.9980999827384949,"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/T10923","display_name":"Force Microscopy Techniques and Applications","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","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"}}],"keywords":[{"id":"https://openalex.org/keywords/rigidity","display_name":"Rigidity (electromagnetism)","score":0.8137818574905396},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7262800335884094},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5221729278564453},{"id":"https://openalex.org/keywords/structural-rigidity","display_name":"Structural rigidity","score":0.5129560828208923},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.4582388401031494},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.38775011897087097},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.36423632502555847},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3536433279514313},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.33018410205841064},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.1658720076084137},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13667577505111694},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09952524304389954}],"concepts":[{"id":"https://openalex.org/C160343418","wikidata":"https://www.wikidata.org/wiki/Q185256","display_name":"Rigidity (electromagnetism)","level":2,"score":0.8137818574905396},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7262800335884094},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5221729278564453},{"id":"https://openalex.org/C155759531","wikidata":"https://www.wikidata.org/wiki/Q7625050","display_name":"Structural rigidity","level":2,"score":0.5129560828208923},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.4582388401031494},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.38775011897087097},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36423632502555847},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3536433279514313},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.33018410205841064},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.1658720076084137},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13667577505111694},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09952524304389954},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","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}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.3390/sym13122401","is_oa":true,"landing_page_url":"https://doi.org/10.3390/sym13122401","pdf_url":"https://www.mdpi.com/2073-8994/13/12/2401/pdf?version=1639539847","source":{"id":"https://openalex.org/S190787756","display_name":"Symmetry","issn_l":"2073-8994","issn":["2073-8994"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Symmetry","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:865a05efa1fa4b94b74ac942b731beb5","is_oa":true,"landing_page_url":"https://doaj.org/article/865a05efa1fa4b94b74ac942b731beb5","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Symmetry, Vol 13, Iss 12, p 2401 (2021)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/2073-8994/13/12/2401/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/sym13122401","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Symmetry","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/sym13122401","is_oa":true,"landing_page_url":"https://doi.org/10.3390/sym13122401","pdf_url":"https://www.mdpi.com/2073-8994/13/12/2401/pdf?version=1639539847","source":{"id":"https://openalex.org/S190787756","display_name":"Symmetry","issn_l":"2073-8994","issn":["2073-8994"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Symmetry","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.7599999904632568}],"awards":[{"id":"https://openalex.org/G409228776","display_name":null,"funder_award_id":"2031283","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4200336584.pdf","grobid_xml":"https://content.openalex.org/works/W4200336584.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W43500862","https://openalex.org/W1974645077","https://openalex.org/W1994337497","https://openalex.org/W2045768640","https://openalex.org/W2051628563","https://openalex.org/W2057400263","https://openalex.org/W2058177295","https://openalex.org/W2065674696","https://openalex.org/W2069308938","https://openalex.org/W2072197675","https://openalex.org/W2075468340","https://openalex.org/W2090338420","https://openalex.org/W2095157453","https://openalex.org/W2109540804","https://openalex.org/W2111989400","https://openalex.org/W2139834426","https://openalex.org/W2142134255","https://openalex.org/W2160426811","https://openalex.org/W2170421654","https://openalex.org/W2280446738","https://openalex.org/W2395832532","https://openalex.org/W2564815219","https://openalex.org/W2607578141","https://openalex.org/W2794224443","https://openalex.org/W3159719254","https://openalex.org/W6712159203"],"related_works":["https://openalex.org/W2117531509","https://openalex.org/W4281491244","https://openalex.org/W1501657243","https://openalex.org/W2376925814","https://openalex.org/W3185639949","https://openalex.org/W2347694834","https://openalex.org/W2626846570","https://openalex.org/W3202031437","https://openalex.org/W1976886486","https://openalex.org/W4210849052"],"abstract_inverted_index":{"Elucidating":[0],"protein":[1,6,12,69,146],"rigidity":[2,30,58],"offers":[3],"insights":[4,22],"about":[5,67,99],"conformational":[7],"changes.":[8],"An":[9],"understanding":[10],"of":[11,27,47,84,104],"motion":[13],"can":[14],"help":[15],"speed":[16],"drug":[17],"development,":[18],"and":[19,60,114,138],"provide":[20],"general":[21],"into":[23],"the":[24,82,85,100,105,112,122],"dynamic":[25],"behaviors":[26],"biomolecules.":[28],"Existing":[29],"analysis":[31],"techniques":[32],"employ":[33],"fine-grained,":[34],"all-atom":[35,77,91,113],"modeling,":[36],"which":[37],"has":[38],"a":[39,68,94,144],"costly":[40],"run-time,":[41],"particularly":[42],"for":[43],"proteins":[44],"made":[45],"up":[46],"more":[48],"than":[49],"500":[50],"residues.":[51],"In":[52],"this":[53],"work,":[54],"we":[55],"introduce":[56],"coarse-grained":[57,86,115,123],"analysis,":[59],"showcase":[61],"that":[62,70,97],"it":[63],"provides":[64,139],"flexibility":[65],"information":[66],"is":[71],"similar":[72,119],"in":[73],"accuracy":[74,83],"to":[75,89],"an":[76,90],"modeling":[78],"approach.":[79],"We":[80],"assess":[81],"method":[87,124],"relative":[88],"approach":[92],"via":[93],"comparison":[95],"metric":[96],"reasons":[98],"largest":[101],"rigid":[102,135],"clusters":[103],"two":[106],"methods.":[107],"The":[108,130],"apparent":[109],"symmetry":[110],"between":[111],"methods":[116],"yields":[117],"very":[118],"results,":[120],"but":[121],"routinely":[125],"exhibits":[126],"40%":[127],"reduced":[128],"run-times.":[129],"CGRAP":[131],"web":[132],"server":[133],"outputs":[134],"cluster":[136],"information,":[137],"data":[140],"visualization":[141],"capabilities,":[142],"including":[143],"interactive":[145],"visualizer.":[147]},"counts_by_year":[{"year":2022,"cited_by_count":2}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
