{"id":"https://openalex.org/W2111643578","doi":"https://doi.org/10.1093/bioinformatics/bti080","title":"A new approach to prediction of short-range conformational propensities in proteins","display_name":"A new approach to prediction of short-range conformational propensities in proteins","publication_year":2004,"publication_date":"2004-10-27","ids":{"openalex":"https://openalex.org/W2111643578","doi":"https://doi.org/10.1093/bioinformatics/bti080","mag":"2111643578","pmid":"https://pubmed.ncbi.nlm.nih.gov/15509604"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti080","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti080","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/7/981/48966608/bioinformatics_21_7_981.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/21/7/981/48966608/bioinformatics_21_7_981.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013884470","display_name":"Dominik Gront","orcid":"https://orcid.org/0000-0002-2260-2083"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Dominik Gront","raw_affiliation_strings":["Faculty of Chemistry, Warsaw University Pasteura 1, 02-093 Warsaw, Poland","Faculty of Chemistry,Warsaw University, Pasteura 1, 02-093 Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Chemistry, Warsaw University Pasteura 1, 02-093 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"Faculty of Chemistry,Warsaw University, Pasteura 1, 02-093 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025085688","display_name":"Andrzej Koli\u0144ski","orcid":"https://orcid.org/0000-0002-8830-2315"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Andrzej Kolinski","raw_affiliation_strings":["Faculty of Chemistry, Warsaw University Pasteura 1, 02-093 Warsaw, Poland","Faculty of Chemistry,Warsaw University, Pasteura 1, 02-093 Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Chemistry, Warsaw University Pasteura 1, 02-093 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"Faculty of Chemistry,Warsaw University, Pasteura 1, 02-093 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5013884470"],"corresponding_institution_ids":["https://openalex.org/I4654613"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.2263,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.52670689,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"21","issue":"7","first_page":"981","last_page":"987"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9147999882698059,"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":0.9147999882698059,"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":0.041999999433755875,"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":0.010999999940395355,"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/range","display_name":"Range (aeronautics)","score":0.6654472947120667},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49736884236335754},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.36564359068870544},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.346768319606781},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19611933827400208},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1303914487361908},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.1247728168964386}],"concepts":[{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.6654472947120667},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49736884236335754},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.36564359068870544},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.346768319606781},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19611933827400208},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1303914487361908},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.1247728168964386},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D008401","descriptor_name":"Gas Chromatography-Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008401","descriptor_name":"Gas Chromatography-Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008401","descriptor_name":"Gas Chromatography-Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","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":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","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":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti080","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti080","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/7/981/48966608/bioinformatics_21_7_981.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:15509604","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15509604","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":"Evaluation Study"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti080","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti080","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/7/981/48966608/bioinformatics_21_7_981.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":[{"id":"https://metadata.un.org/sdg/7","score":0.7799999713897705,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2111643578.pdf","grobid_xml":"https://content.openalex.org/works/W2111643578.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1969051510","https://openalex.org/W1985818354","https://openalex.org/W2008708467","https://openalex.org/W2016411902","https://openalex.org/W2087064593","https://openalex.org/W2097546936","https://openalex.org/W2113993025","https://openalex.org/W2117647295","https://openalex.org/W2118495244","https://openalex.org/W2120813534","https://openalex.org/W2128577591","https://openalex.org/W2151631782","https://openalex.org/W2153153865","https://openalex.org/W2153187042","https://openalex.org/W2154106236","https://openalex.org/W2158714788","https://openalex.org/W2166924104","https://openalex.org/W6682889726"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"MOTIVATION:":[0],"Knowledge-based":[1],"potentials":[2,48,117],"are":[3],"valuable":[4,51],"tools":[5],"for":[6,74],"protein":[7,44,57,77,92,129],"structure":[8,17,58,63],"modeling":[9,61,64],"and":[10,62,81,121,136],"evaluation":[11],"of":[12,15,23,26,37,53,90,98,104,115,128],"the":[13,16,38,88,105,113,122,138],"quality":[14],"prediction":[18],"obtained":[19],"by":[20,33,95],"a":[21,34],"variety":[22],"methods.":[24],"Potentials":[25],"such":[27],"type":[28],"could":[29,49],"be":[30,50],"significantly":[31],"enhanced":[32],"proper":[35],"exploitation":[36],"evolutionary":[39],"information":[40],"encoded":[41],"in":[42,133,137],"related":[43],"sequences.":[45],"The":[46,83],"new":[47,72],"components":[52],"threading":[54,120,134],"algorithms,":[55],"ab-initio":[56],"prediction,":[59],"comparative":[60],"based":[65,86],"on":[66,87],"fragmentary":[67],"experimental":[68],"data.":[69],"RESULTS:":[70],"A":[71],"potential":[73],"scoring":[75],"local":[76],"geometry":[78,127],"is":[79,85],"designed":[80],"evaluated.":[82],"approach":[84],"similarity":[89],"short":[91],"fragments":[93],"measured":[94],"an":[96],"alignment":[97],"their":[99],"sequence":[100],"profiles.":[101],"Sequence":[102],"specificity":[103,114],"resulting":[106],"energy":[107],"function":[108],"has":[109,145],"been":[110,146],"compared":[111],"with":[112],"simpler":[116],"using":[118],"gapless":[119],"ability":[123,139],"to":[124,140],"predict":[125],"specific":[126],"fragments.":[130],"Significant":[131],"improvement":[132],"sensitivity":[135],"generate":[141],"sequence-specific":[142],"protein-like":[143],"conformations":[144],"achieved.":[147]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
