{"id":"https://openalex.org/W4375863182","doi":"https://doi.org/10.1007/s11047-023-09943-4","title":"Protein structure prediction with energy minimization and deep learning approaches","display_name":"Protein structure prediction with energy minimization and deep learning approaches","publication_year":2023,"publication_date":"2023-05-08","ids":{"openalex":"https://openalex.org/W4375863182","doi":"https://doi.org/10.1007/s11047-023-09943-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/37363286"},"language":"en","primary_location":{"id":"doi:10.1007/s11047-023-09943-4","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s11047-023-09943-4","pdf_url":"https://link.springer.com/content/pdf/10.1007/s11047-023-09943-4.pdf","source":{"id":"https://openalex.org/S149828480","display_name":"Natural Computing","issn_l":"1567-7818","issn":["1567-7818","1572-9796"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Natural Computing","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s11047-023-09943-4.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021799631","display_name":"Juan Luis Filgueiras","orcid":null},"institutions":[{"id":"https://openalex.org/I11019714","display_name":"Universidade da Coru\u00f1a","ror":"https://ror.org/01qckj285","country_code":"ES","type":"education","lineage":["https://openalex.org/I11019714"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Juan Luis Filgueiras","raw_affiliation_strings":["Department of Computer Science and Information Technologies, CITIC (Centre for Information and Communications Technology Research), University of A Coru\u00f1a, A Coru\u00f1a, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Technologies, CITIC (Centre for Information and Communications Technology Research), University of A Coru\u00f1a, A Coru\u00f1a, Spain","institution_ids":["https://openalex.org/I11019714"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059664152","display_name":"Daniel Varela","orcid":"https://orcid.org/0000-0001-7799-0119"},"institutions":[{"id":"https://openalex.org/I11019714","display_name":"Universidade da Coru\u00f1a","ror":"https://ror.org/01qckj285","country_code":"ES","type":"education","lineage":["https://openalex.org/I11019714"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Daniel Varela","raw_affiliation_strings":["Department of Computer Science and Information Technologies, CITIC (Centre for Information and Communications Technology Research), University of A Coru\u00f1a, A Coru\u00f1a, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Technologies, CITIC (Centre for Information and Communications Technology Research), University of A Coru\u00f1a, A Coru\u00f1a, Spain","institution_ids":["https://openalex.org/I11019714"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089427591","display_name":"Jos\u00e9 S\u00e1ntos","orcid":"https://orcid.org/0000-0002-4212-1367"},"institutions":[{"id":"https://openalex.org/I11019714","display_name":"Universidade da Coru\u00f1a","ror":"https://ror.org/01qckj285","country_code":"ES","type":"education","lineage":["https://openalex.org/I11019714"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 Santos","raw_affiliation_strings":["Department of Computer Science and Information Technologies, CITIC (Centre for Information and Communications Technology Research), University of A Coru\u00f1a, A Coru\u00f1a, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Technologies, CITIC (Centre for Information and Communications Technology Research), University of A Coru\u00f1a, A Coru\u00f1a, Spain","institution_ids":["https://openalex.org/I11019714"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5021799631"],"corresponding_institution_ids":["https://openalex.org/I11019714"],"apc_list":{"value":2890,"currency":"USD","value_usd":2890},"apc_paid":{"value":2890,"currency":"USD","value_usd":2890},"fwci":1.0299,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.73933679,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"22","issue":"4","first_page":"659","last_page":"670"},"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":0.9983999729156494,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9983999729156494,"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/energy-minimization","display_name":"Energy minimization","score":0.6487936973571777},{"id":"https://openalex.org/keywords/theory-of-computation","display_name":"Theory of computation","score":0.6397488117218018},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6286008954048157},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6248916983604431},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.619331419467926},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5133799314498901},{"id":"https://openalex.org/keywords/minification","display_name":"Minification","score":0.4912356734275818},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.49105095863342285},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.42404696345329285},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.2393677532672882},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2026941180229187},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16977158188819885},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.12430772185325623},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.11492481827735901},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.10007166862487793},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.07786953449249268}],"concepts":[{"id":"https://openalex.org/C14961307","wikidata":"https://www.wikidata.org/wiki/Q5377176","display_name":"Energy minimization","level":2,"score":0.6487936973571777},{"id":"https://openalex.org/C24858836","wikidata":"https://www.wikidata.org/wiki/Q844718","display_name":"Theory of computation","level":2,"score":0.6397488117218018},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6286008954048157},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6248916983604431},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.619331419467926},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5133799314498901},{"id":"https://openalex.org/C147764199","wikidata":"https://www.wikidata.org/wiki/Q6865248","display_name":"Minification","level":2,"score":0.4912356734275818},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.49105095863342285},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.42404696345329285},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2393677532672882},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2026941180229187},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16977158188819885},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.12430772185325623},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.11492481827735901},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.10007166862487793},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.07786953449249268},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1007/s11047-023-09943-4","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s11047-023-09943-4","pdf_url":"https://link.springer.com/content/pdf/10.1007/s11047-023-09943-4.pdf","source":{"id":"https://openalex.org/S149828480","display_name":"Natural Computing","issn_l":"1567-7818","issn":["1567-7818","1572-9796"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Natural Computing","raw_type":"journal-article"},{"id":"pmid:37363286","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37363286","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Natural computing","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10165305","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10165305","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10165305/pdf/11047_2023_Article_9943.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"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":"Nat Comput","raw_type":"Text"},{"id":"pmh:oai:ruc.udc.es:2183/37418","is_oa":true,"landing_page_url":"http://hdl.handle.net/2183/37418","pdf_url":null,"source":{"id":"https://openalex.org/S4306402204","display_name":"RUC (Universidade Da Coru\u00f1a)","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1007/s11047-023-09943-4","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s11047-023-09943-4","pdf_url":"https://link.springer.com/content/pdf/10.1007/s11047-023-09943-4.pdf","source":{"id":"https://openalex.org/S149828480","display_name":"Natural Computing","issn_l":"1567-7818","issn":["1567-7818","1572-9796"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Natural Computing","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.800000011920929,"id":"https://metadata.un.org/sdg/7"}],"awards":[{"id":"https://openalex.org/G1885417913","display_name":null,"funder_award_id":"GPC ED431B 2022/33","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G1933851018","display_name":null,"funder_award_id":"ED431G 2019/01","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G2462709576","display_name":null,"funder_award_id":"CITIC (ED431G 2019/01)","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G2979118188","display_name":null,"funder_award_id":"PID2020-116201GB-I00","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G3199046289","display_name":null,"funder_award_id":"ED431G 2019/01","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3876637791","display_name":null,"funder_award_id":"ED431G","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G5634946813","display_name":null,"funder_award_id":"2014-2020","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G5805502524","display_name":null,"funder_award_id":"PID2020","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G6258374248","display_name":null,"funder_award_id":"ED431B","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G6589649124","display_name":null,"funder_award_id":"PID2020-","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G6870533126","display_name":null,"funder_award_id":"2014-2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G726424357","display_name":null,"funder_award_id":"ED431G 2019/01","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G7683671810","display_name":null,"funder_award_id":"PID2020- 116201GB-I00","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320326655","display_name":"Xunta de Galicia","ror":"https://ror.org/0181xnw06"},{"id":"https://openalex.org/F4320328562","display_name":"Universidade da Coru\u00f1a","ror":"https://ror.org/01qckj285"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4375863182.pdf"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W200248288","https://openalex.org/W1548178570","https://openalex.org/W2033650210","https://openalex.org/W2045777307","https://openalex.org/W2056760934","https://openalex.org/W2140673705","https://openalex.org/W2292696179","https://openalex.org/W2337606518","https://openalex.org/W2765460169","https://openalex.org/W2944489523","https://openalex.org/W2950954328","https://openalex.org/W2997234557","https://openalex.org/W2999044305","https://openalex.org/W3177828909","https://openalex.org/W3183475563","https://openalex.org/W3186179742","https://openalex.org/W4206002704","https://openalex.org/W4206940890","https://openalex.org/W4220887157","https://openalex.org/W4223956519","https://openalex.org/W4281790889","https://openalex.org/W4285169958","https://openalex.org/W4309094945"],"related_works":["https://openalex.org/W1518796764","https://openalex.org/W2118841422","https://openalex.org/W347294048","https://openalex.org/W2226908759","https://openalex.org/W1899667806","https://openalex.org/W2158144798","https://openalex.org/W2061881449","https://openalex.org/W1981231660","https://openalex.org/W2351116219","https://openalex.org/W2110536527"],"abstract_inverted_index":{"In":[0,59],"this":[1,60],"paper":[2],"we":[3],"discuss":[4],"the":[5,42,74,82,87,97],"advantages":[6],"and":[7,52,73,99],"problems":[8],"of":[9,37,84,106,108],"two":[10],"alternatives":[11],"for":[12,33],"ab":[13],"initio":[14],"protein":[15,48],"structure":[16],"prediction.":[17],"On":[18,41],"one":[19],"hand,":[20,44],"recent":[21],"approaches":[22],"based":[23,46,65],"on":[24,47,66],"deep":[25],"learning,":[26],"which":[27],"have":[28,92],"significantly":[29],"improved":[30],"prediction":[31],"results":[32],"a":[34,67],"wide":[35],"variety":[36],"proteins,":[38],"are":[39,57,78],"discussed.":[40],"other":[43],"methods":[45,64],"conformational":[49],"energy":[50],"minimization":[51],"with":[53],"different":[54],"search":[55],"strategies":[56],"analyzed.":[58],"latter":[61],"case,":[62],"our":[63],"memetic":[68],"combination":[69],"between":[70],"differential":[71],"evolution":[72],"fragment":[75],"replacement":[76],"technique":[77],"included,":[79],"incorporating":[80],"also":[81],"possibility":[83],"niching":[85],"in":[86,101],"evolutionary":[88],"search.":[89],"Different":[90],"proteins":[91],"been":[93],"used":[94],"to":[95],"analyze":[96],"pros":[98],"cons":[100],"both":[102,109],"approaches,":[103],"proposing":[104],"possibilities":[105],"integration":[107],"alternatives.":[110]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
