{"id":"https://openalex.org/W2128847211","doi":"https://doi.org/10.1109/cibcb.2006.330978","title":"P-found: The Protein Folding and Unfolding Simulation Repository","display_name":"P-found: The Protein Folding and Unfolding Simulation Repository","publication_year":2006,"publication_date":"2006-09-01","ids":{"openalex":"https://openalex.org/W2128847211","doi":"https://doi.org/10.1109/cibcb.2006.330978","mag":"2128847211"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb.2006.330978","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2006.330978","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology","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/A5005828840","display_name":"C\u00e2ndida G. Silva","orcid":"https://orcid.org/0000-0002-7092-1169"},"institutions":[{"id":"https://openalex.org/I76903346","display_name":"University of Coimbra","ror":"https://ror.org/04z8k9a98","country_code":"PT","type":"education","lineage":["https://openalex.org/I76903346"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Candida G. Silva","raw_affiliation_strings":["Chemistry Department, Faculty of Science and Technology, and Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal","Chem. Dept., Coimbra Univ"],"affiliations":[{"raw_affiliation_string":"Chemistry Department, Faculty of Science and Technology, and Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal","institution_ids":["https://openalex.org/I76903346"]},{"raw_affiliation_string":"Chem. Dept., Coimbra Univ","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061569269","display_name":"Vitaliy Ostropytskyy","orcid":null},"institutions":[{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Vitaliy Ostropytskyy","raw_affiliation_strings":["School of Biomedical Sciences, University of Ulster, Coleraine, UK","School of Biomedical Sciences, University of Ulster, Cromore Road, BT52 1SA Coleraine, Northern Ireland"],"affiliations":[{"raw_affiliation_string":"School of Biomedical Sciences, University of Ulster, Coleraine, UK","institution_ids":["https://openalex.org/I138801177"]},{"raw_affiliation_string":"School of Biomedical Sciences, University of Ulster, Cromore Road, BT52 1SA Coleraine, Northern Ireland","institution_ids":["https://openalex.org/I138801177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083588473","display_name":"Nuno Loureiro\u2010Ferreira","orcid":null},"institutions":[{"id":"https://openalex.org/I76903346","display_name":"University of Coimbra","ror":"https://ror.org/04z8k9a98","country_code":"PT","type":"education","lineage":["https://openalex.org/I76903346"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Nuno Loureiro-Ferreira","raw_affiliation_strings":["Chemistry Department, Faculty of Science and Technology, and Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal","Chemistry Department, Faculty of Science and Technology, and Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal#TAB#"],"affiliations":[{"raw_affiliation_string":"Chemistry Department, Faculty of Science and Technology, and Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal","institution_ids":["https://openalex.org/I76903346"]},{"raw_affiliation_string":"Chemistry Department, Faculty of Science and Technology, and Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal#TAB#","institution_ids":["https://openalex.org/I76903346"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091132218","display_name":"Daniel Berrar","orcid":"https://orcid.org/0000-0002-7038-2601"},"institutions":[{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Daniel Berrar","raw_affiliation_strings":["School of Biomedical Sciences, University of Ulster, Coleraine, UK","School of Biomedical Sciences, University of Ulster, Cromore Road, BT52 1SA Coleraine, Northern Ireland"],"affiliations":[{"raw_affiliation_string":"School of Biomedical Sciences, University of Ulster, Coleraine, UK","institution_ids":["https://openalex.org/I138801177"]},{"raw_affiliation_string":"School of Biomedical Sciences, University of Ulster, Cromore Road, BT52 1SA Coleraine, Northern Ireland","institution_ids":["https://openalex.org/I138801177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000794908","display_name":"Martin Swain","orcid":"https://orcid.org/0000-0002-1418-4440"},"institutions":[{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Martin Swain","raw_affiliation_strings":["School of Biomedical Sciences, University of Ulster, Coleraine, UK","School of Biomedical Sciences, University of Ulster, Cromore Road, BT52 1SA Coleraine, Northern Ireland"],"affiliations":[{"raw_affiliation_string":"School of Biomedical Sciences, University of Ulster, Coleraine, UK","institution_ids":["https://openalex.org/I138801177"]},{"raw_affiliation_string":"School of Biomedical Sciences, University of Ulster, Cromore Road, BT52 1SA Coleraine, Northern Ireland","institution_ids":["https://openalex.org/I138801177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011609464","display_name":"Werner Dubitzky","orcid":null},"institutions":[{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Werner Dubitzky","raw_affiliation_strings":["School of Biomedical Sciences, University of Ulster, Coleraine, UK","School of Biomedical Sciences, University of Ulster, Cromore Road, BT52 1SA Coleraine, Northern Ireland. Email: w.dubitzky@ulster.ac.uk"],"affiliations":[{"raw_affiliation_string":"School of Biomedical Sciences, University of Ulster, Coleraine, UK","institution_ids":["https://openalex.org/I138801177"]},{"raw_affiliation_string":"School of Biomedical Sciences, University of Ulster, Cromore Road, BT52 1SA Coleraine, Northern Ireland. Email: w.dubitzky@ulster.ac.uk","institution_ids":["https://openalex.org/I138801177"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088910380","display_name":"Rui M. M. Brito","orcid":"https://orcid.org/0000-0001-9128-2557"},"institutions":[{"id":"https://openalex.org/I76903346","display_name":"University of Coimbra","ror":"https://ror.org/04z8k9a98","country_code":"PT","type":"education","lineage":["https://openalex.org/I76903346"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Rui M. M. Brito","raw_affiliation_strings":["Chemistry Department, Faculty of Science and Technology, and Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal","Chemistry Department, Faculty of Science and Technology, and Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal. Email: brito@ci.uc.pt"],"affiliations":[{"raw_affiliation_string":"Chemistry Department, Faculty of Science and Technology, and Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal","institution_ids":["https://openalex.org/I76903346"]},{"raw_affiliation_string":"Chemistry Department, Faculty of Science and Technology, and Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal. Email: brito@ci.uc.pt","institution_ids":["https://openalex.org/I76903346"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5005828840"],"corresponding_institution_ids":["https://openalex.org/I76903346"],"apc_list":null,"apc_paid":null,"fwci":0.5298,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.64673666,"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":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9991000294685364,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9973999857902527,"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/upload","display_name":"Upload","score":0.7441794872283936},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6884256601333618},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.621994137763977},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.5823017954826355},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.49956607818603516},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.49061813950538635},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40349090099334717},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.362345814704895},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2665250301361084},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1470363736152649},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.12188839912414551},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09680971503257751},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08454793691635132},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07222941517829895}],"concepts":[{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.7441794872283936},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6884256601333618},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.621994137763977},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.5823017954826355},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.49956607818603516},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.49061813950538635},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40349090099334717},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.362345814704895},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2665250301361084},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1470363736152649},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.12188839912414551},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09680971503257751},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08454793691635132},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07222941517829895},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cibcb.2006.330978","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2006.330978","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.6399999856948853,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1575681173","https://openalex.org/W1597461969","https://openalex.org/W1981021420","https://openalex.org/W2019096787","https://openalex.org/W2022535690","https://openalex.org/W2029667189","https://openalex.org/W2070875588","https://openalex.org/W2083416535","https://openalex.org/W2093381148","https://openalex.org/W2103032510","https://openalex.org/W2103815459","https://openalex.org/W2130479394","https://openalex.org/W2134342348","https://openalex.org/W2159010139","https://openalex.org/W2160721947","https://openalex.org/W2162166182","https://openalex.org/W2478173465"],"related_works":["https://openalex.org/W1673912714","https://openalex.org/W2260493136","https://openalex.org/W2113188411","https://openalex.org/W2976965029","https://openalex.org/W2382178265","https://openalex.org/W2055827177","https://openalex.org/W2072666835","https://openalex.org/W4248706500","https://openalex.org/W1999927713","https://openalex.org/W2939859775"],"abstract_inverted_index":{"One":[0],"of":[1,18,22,29,55,94,98,103,134,154,163,188],"the":[2,11,16,19,48,53,92,96,127,129,150,167,198],"central":[3],"challenges":[4],"in":[5,73],"structural":[6],"molecular":[7,135,156],"biology":[8],"today":[9],"is":[10,59,124,201],"protein":[12,24,36,39,108,111,118,121,138],"folding":[13,37,109,119,139],"problem,":[14],"i.e.":[15],"acquisition":[17],"3D":[20],"structure":[21],"a":[23,87],"from":[25],"its":[26],"linear":[27],"sequence":[28],"amino-acids.":[30],"Different":[31],"computational":[32],"approaches":[33],"to":[34,47,52,62,85],"study":[35],"and":[38,101,105,110,120,140,144,158,161,180,186],"unfolding":[40,112,122,141],"have":[41],"recently":[42],"become":[43],"common":[44],"tools":[45],"available":[46],"researcher.":[49],"However,":[50],"due":[51],"lack":[54],"appropriate":[56],"infrastructures,":[57],"it":[58],"very":[60],"difficult":[61],"directly":[63],"compare":[64],"simulations":[65,123,170,190],"performed":[66,171],"by":[67,172],"different":[68,71,74,79],"groups,":[69],"with":[70,91,149],"methods,":[72],"experimental":[75],"conditions":[76],"or":[77],"for":[78,117,184,197],"proteins.":[80],"Thus,":[81],"we":[82],"set":[83],"out":[84],"create":[86],"public":[88],"data":[89,106,130,181],"repository":[90,131],"goal":[93],"addressing":[95],"problem":[97],"comparison,":[99],"analysis":[100,185],"sharing":[102],"information":[104],"on":[107],"simulations.":[113],"The":[114,194],"P-found":[115,199],"system":[116,200],"presented.":[125],"At":[126],"moment,":[128],"allows":[132,159],"uploading":[133],"dynamics":[136],"(MD)":[137],"simulations,":[142],"calculates":[143],"stores":[145],"several":[146],"time":[147,153],"series":[148],"variation":[151],"over":[152],"pre-defined":[155],"properties,":[157],"searching":[160],"downloading":[162],"these":[164],"data.":[165],"In":[166],"near":[168],"future,":[169],"other":[173],"than":[174],"MD":[175],"methods":[176],"may":[177],"be":[178,192],"uploaded,":[179],"mining":[182],"techniques":[183],"comparison":[187],"multiple":[189],"will":[191],"implemented.":[193],"home":[195],"page":[196],"accessible":[202],"at":[203],"http://www.p-found.org":[204]},"counts_by_year":[{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
