{"id":"https://openalex.org/W2147736339","doi":"https://doi.org/10.1145/2506583.2506680","title":"Automated protein structure refinement using i3Drefine software and its assessment in CASP10","display_name":"Automated protein structure refinement using i3Drefine software and its assessment in CASP10","publication_year":2013,"publication_date":"2013-09-22","ids":{"openalex":"https://openalex.org/W2147736339","doi":"https://doi.org/10.1145/2506583.2506680","mag":"2147736339"},"language":"en","primary_location":{"id":"doi:10.1145/2506583.2506680","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506680","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","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/A5018409409","display_name":"Debswapna Bhattacharya","orcid":"https://orcid.org/0000-0002-9630-0141"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Debswapna Bhattacharya","raw_affiliation_strings":["Department of Computer Science, University of Missouri, Columbia, MO 65211, USA, +1-(801)-819-5828"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Missouri, Columbia, MO 65211, USA, +1-(801)-819-5828","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044354277","display_name":"Jianlin Cheng","orcid":"https://orcid.org/0000-0003-0305-2853"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianlin Cheng","raw_affiliation_strings":["Department of Computer Science, Informatics Institute, C. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA, +1-(573)-882-7306"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Informatics Institute, C. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA, +1-(573)-882-7306","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I76835614"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10996218,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"678","last_page":"678"},"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":0.9998000264167786,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9973000288009644,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/executable","display_name":"Executable","score":0.8250458240509033},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7938246726989746},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5133303999900818},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.4616680443286896},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.44441288709640503},{"id":"https://openalex.org/keywords/energy-minimization","display_name":"Energy minimization","score":0.444023460149765},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3763900697231293},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36988818645477295},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.22977125644683838},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1733473539352417},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14477035403251648},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.07986223697662354}],"concepts":[{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.8250458240509033},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7938246726989746},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5133303999900818},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.4616680443286896},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.44441288709640503},{"id":"https://openalex.org/C14961307","wikidata":"https://www.wikidata.org/wiki/Q5377176","display_name":"Energy minimization","level":2,"score":0.444023460149765},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3763900697231293},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36988818645477295},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.22977125644683838},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1733473539352417},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14477035403251648},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.07986223697662354},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2506583.2506680","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506680","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.6499999761581421}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2350278424","https://openalex.org/W2366107444","https://openalex.org/W2071432835","https://openalex.org/W4239401009","https://openalex.org/W4234371507","https://openalex.org/W1628824497","https://openalex.org/W2158562723","https://openalex.org/W4285169958","https://openalex.org/W2090758793","https://openalex.org/W4318263509"],"abstract_inverted_index":{"We":[0],"present":[1],"fully":[2],"automated":[3],"and":[4,18,30,34,91],"computationally":[5],"efficient":[6],"protein":[7],"3D":[8],"structure":[9],"refinement":[10],"software":[11,100],"called":[12],"i3Drefine,":[13],"based":[14],"on":[15],"an":[16],"iterative":[17],"highly":[19],"convergent":[20],"energy":[21],"minimization":[22],"algorithm":[23],"with":[24],"a":[25],"powerful":[26],"all-atom":[27],"composite":[28],"physics":[29],"knowledge-based":[31],"force":[32],"fields":[33],"hydrogen":[35],"bonding":[36],"(HB)":[37],"network":[38],"optimization":[39],"technique.":[40],"In":[41],"the":[42,54,58,63,85],"recent":[43],"community-wide":[44],"blind":[45],"experiment,":[46],"CASP10,":[47],"i3Drefine":[48,73,99],"(as":[49],"'MULTICOM-CONSTRUCT')":[50],"was":[51],"ranked":[52],"as":[53,61],"best":[55],"method":[56],"in":[57,79,88],"server":[59,77],"section":[60],"per":[62],"official":[64],"assessment":[65],"of":[66,98],"CASP10":[67,80],"experiment.":[68],"Our":[69],"analysis":[70],"demonstrates":[71],"that":[72],"is":[74,101],"only":[75],"fully-automated":[76],"participating":[78],"exhibiting":[81],"consistent":[82],"improvement":[83],"over":[84],"initial":[86],"structures":[87],"both":[89],"global":[90],"local":[92],"structural":[93],"quality":[94],"metrics.":[95],"Executable":[96],"version":[97],"freely":[102],"available":[103],"at":[104],"http://protein.rnet.missouri.edu/i3drefine/.":[105]},"counts_by_year":[],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}
