{"id":"https://openalex.org/W2145420798","doi":"https://doi.org/10.1093/bioinformatics/btp449","title":"Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential","display_name":"Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential","publication_year":2009,"publication_date":"2009-07-23","ids":{"openalex":"https://openalex.org/W2145420798","doi":"https://doi.org/10.1093/bioinformatics/btp449","mag":"2145420798","pmid":"https://pubmed.ncbi.nlm.nih.gov/19628506"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp449","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp449","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/20/2639/48995260/bioinformatics_25_20_2639.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/20/2639/48995260/bioinformatics_25_20_2639.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004802142","display_name":"Ami Levy\u2010Moonshine","orcid":null},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Ami Levy-Moonshine","raw_affiliation_strings":["1 Department of Computer Science and 2 Department of Life Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science and 2 Department of Life Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080001526","display_name":"El-ad David Amir","orcid":null},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"El-ad David Amir","raw_affiliation_strings":["1 Department of Computer Science and 2 Department of Life Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science and 2 Department of Life Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072753313","display_name":"Chen Keasar","orcid":"https://orcid.org/0000-0003-0994-1520"},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Chen Keasar","raw_affiliation_strings":["1 Department of Computer Science and 2 Department of Life Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science and 2 Department of Life Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel","institution_ids":["https://openalex.org/I124227911"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.2739,"has_fulltext":true,"cited_by_count":38,"citation_normalized_percentile":{"value":0.61266344,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"25","issue":"20","first_page":"2639","last_page":"2645"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9129999876022339,"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":0.9129999876022339,"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":0.01759999990463257,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.004800000227987766,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/hydrogen-bond","display_name":"Hydrogen bond","score":0.7363465428352356},{"id":"https://openalex.org/keywords/beta-sheet","display_name":"Beta sheet","score":0.7045559287071228},{"id":"https://openalex.org/keywords/beta","display_name":"BETA (programming language)","score":0.5502254962921143},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.508152961730957},{"id":"https://openalex.org/keywords/term","display_name":"Term (time)","score":0.5060424208641052},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.41411495208740234},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.37478625774383545},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3433535695075989},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.33056408166885376},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.32550108432769775},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.3224726617336273},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2821214497089386},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.2433643341064453},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.215020090341568},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10089927911758423}],"concepts":[{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.7363465428352356},{"id":"https://openalex.org/C159547669","wikidata":"https://www.wikidata.org/wiki/Q283449","display_name":"Beta sheet","level":3,"score":0.7045559287071228},{"id":"https://openalex.org/C2776174256","wikidata":"https://www.wikidata.org/wiki/Q830842","display_name":"BETA (programming language)","level":2,"score":0.5502254962921143},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.508152961730957},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.5060424208641052},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.41411495208740234},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.37478625774383545},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3433535695075989},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.33056408166885376},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.32550108432769775},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.3224726617336273},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2821214497089386},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.2433643341064453},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.215020090341568},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10089927911758423},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btp449","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp449","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/20/2639/48995260/bioinformatics_25_20_2639.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19628506","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19628506","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.1007.8461","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1007.8461","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2009/07/23/bioinformatics.btp449.full.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3140807","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3140807","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp449","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp449","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/20/2639/48995260/bioinformatics_25_20_2639.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6600000262260437,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2145420798.pdf","grobid_xml":"https://content.openalex.org/works/W2145420798.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W123045926","https://openalex.org/W1528852144","https://openalex.org/W1543736827","https://openalex.org/W1546962148","https://openalex.org/W1965838279","https://openalex.org/W1968543088","https://openalex.org/W1971251199","https://openalex.org/W1978578758","https://openalex.org/W1979046104","https://openalex.org/W1979670056","https://openalex.org/W1990700294","https://openalex.org/W2003811416","https://openalex.org/W2004058380","https://openalex.org/W2004461664","https://openalex.org/W2008708467","https://openalex.org/W2013785414","https://openalex.org/W2015392953","https://openalex.org/W2016610222","https://openalex.org/W2024060531","https://openalex.org/W2028702957","https://openalex.org/W2041189078","https://openalex.org/W2045127155","https://openalex.org/W2050595677","https://openalex.org/W2051434435","https://openalex.org/W2051628563","https://openalex.org/W2068970274","https://openalex.org/W2072292331","https://openalex.org/W2075468261","https://openalex.org/W2076488922","https://openalex.org/W2085277871","https://openalex.org/W2085822586","https://openalex.org/W2087149342","https://openalex.org/W2089298522","https://openalex.org/W2103159791","https://openalex.org/W2105243761","https://openalex.org/W2108067237","https://openalex.org/W2114441129","https://openalex.org/W2122199548","https://openalex.org/W2130479394","https://openalex.org/W2134059200","https://openalex.org/W2134812230","https://openalex.org/W2141988096","https://openalex.org/W2142134255","https://openalex.org/W2145358391","https://openalex.org/W2148946251","https://openalex.org/W2150705899","https://openalex.org/W2159618687","https://openalex.org/W2162166182","https://openalex.org/W2163333444","https://openalex.org/W2317800347","https://openalex.org/W2323178299","https://openalex.org/W4242855320","https://openalex.org/W6645217179"],"related_works":["https://openalex.org/W1525746053","https://openalex.org/W2043259878","https://openalex.org/W2760940816","https://openalex.org/W2090443083","https://openalex.org/W3115195615","https://openalex.org/W2062744088","https://openalex.org/W2101817300","https://openalex.org/W2072355506","https://openalex.org/W2505421132","https://openalex.org/W2049099547"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,139],"roughness":[2],"of":[3,39,47,110],"energy":[4],"landscapes":[5],"is":[6,31,84,99,142,149],"a":[7,78,126],"major":[8],"obstacle":[9],"to":[10,19,24,33,118],"protein":[11,105],"structure":[12,132],"prediction,":[13],"since":[14,35],"it":[15],"forces":[16],"conformational":[17],"searches":[18],"spend":[20],"much":[21],"time":[22],"struggling":[23],"escape":[25],"numerous":[26],"traps.":[27],"Specifically,":[28],"beta-sheet":[29,48,121],"formation":[30],"prone":[32],"stray,":[34],"many":[36],"possible":[37],"combinations":[38],"hydrogen":[40,59,66],"bonds":[41,60],"are":[42,70],"dead":[43],"ends":[44],"in":[45,87],"terms":[46,56],"assembly.":[49],"It":[50],"has":[51],"been":[52],"shown":[53],"that":[54,69,83],"cooperative":[55,80],"for":[57],"backbone":[58],"ease":[61],"this":[62],"problem":[63],"by":[64],"augmenting":[65],"bond":[67],"patterns":[68],"consistent":[71],"with":[72],"beta":[73,89],"sheets.":[74],"Here,":[75],"we":[76],"present":[77],"novel":[79],"hydrogen-bond":[81],"term":[82,98,116,141],"both":[85],"effective":[86],"promoting":[88],"sheets":[90],"and":[91,101,148],"computationally":[92],"efficient.":[93],"In":[94],"addition,":[95],"the":[96,114,130,145],"new":[97,115,140],"differentiable":[100],"operates":[102],"on":[103],"all-atom":[104],"models.":[106],"RESULTS:":[107],"Energy":[108],"optimization":[109,124],"poly-alanine":[111],"chains":[112],"under":[113,125],"led":[117],"significantly":[119],"more":[120],"content":[122],"than":[123],"non-cooperative":[127],"term.":[128],"Furthermore,":[129],"optimized":[131],"included":[133],"very":[134],"few":[135],"non-native":[136],"patterns.":[137],"AVAILABILITY:":[138],"implemented":[143],"within":[144],"MESHI":[146],"package":[147],"freely":[150],"available":[151],"at":[152],"http://cs.bgu.ac.il/":[153],"approximately":[154],"meshi.":[155]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
