{"id":"https://openalex.org/W2019119537","doi":"https://doi.org/10.1142/s0219720008003783","title":"LONG-RANGE INFORMATION AND PHYSICALITY CONSTRAINTS IMPROVE PREDICTED PROTEIN CONTACT MAPS","display_name":"LONG-RANGE INFORMATION AND PHYSICALITY CONSTRAINTS IMPROVE PREDICTED PROTEIN CONTACT MAPS","publication_year":2008,"publication_date":"2008-10-01","ids":{"openalex":"https://openalex.org/W2019119537","doi":"https://doi.org/10.1142/s0219720008003783","mag":"2019119537","pmid":"https://pubmed.ncbi.nlm.nih.gov/18942163"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720008003783","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720008003783","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5022019480","display_name":"Alberto J. M. Mart\u00edn","orcid":"https://orcid.org/0000-0002-6147-3325"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"ALBERTO J. M. MARTIN","raw_affiliation_strings":["Complex and Adaptive Systems Lab, School of Computer Science and Informatics, University College Dublin, Belfield, Dublin 4, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Complex and Adaptive Systems Lab, School of Computer Science and Informatics, University College Dublin, Belfield, Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066061347","display_name":"Davide Ba\u00f9","orcid":"https://orcid.org/0000-0002-4177-2838"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"DAVIDE BA\u00d9","raw_affiliation_strings":["Complex and Adaptive Systems Lab, School of Computer Science and Informatics, University College Dublin, Belfield, Dublin 4, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Complex and Adaptive Systems Lab, School of Computer Science and Informatics, University College Dublin, Belfield, Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086404635","display_name":"Alessandro Vullo","orcid":"https://orcid.org/0000-0002-8237-5660"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"ALESSANDRO VULLO","raw_affiliation_strings":["Complex and Adaptive Systems Lab, School of Computer Science and Informatics, University College Dublin, Belfield, Dublin 4, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Complex and Adaptive Systems Lab, School of Computer Science and Informatics, University College Dublin, Belfield, Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060625212","display_name":"Ian Walsh","orcid":"https://orcid.org/0000-0003-3994-5522"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"IAN WALSH","raw_affiliation_strings":["Complex and Adaptive Systems Lab, School of Computer Science and Informatics, University College Dublin, Belfield, Dublin 4, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Complex and Adaptive Systems Lab, School of Computer Science and Informatics, University College Dublin, Belfield, Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016630267","display_name":"Gianluca Pollastri","orcid":"https://orcid.org/0000-0002-5825-4949"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"GIANLUCA POLLASTRI","raw_affiliation_strings":["Complex and Adaptive Systems Lab, School of Computer Science and Informatics, University College Dublin, Belfield, Dublin 4, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Complex and Adaptive Systems Lab, School of Computer Science and Informatics, University College Dublin, Belfield, Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.2808,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.59964739,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"06","issue":"05","first_page":"1001","last_page":"1020"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9908999800682068,"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":0.9894999861717224,"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/computer-science","display_name":"Computer science","score":0.5592477321624756},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.5554754734039307},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.5332647562026978},{"id":"https://openalex.org/keywords/ab-initio","display_name":"Ab initio","score":0.4795803129673004},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.47354358434677124},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.47129762172698975},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.46318650245666504},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.37174805998802185},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.34868931770324707},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.25682997703552246},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.13341552019119263},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1296217143535614},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1225791871547699},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.07934194803237915}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5592477321624756},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.5554754734039307},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.5332647562026978},{"id":"https://openalex.org/C2781442258","wikidata":"https://www.wikidata.org/wiki/Q46310","display_name":"Ab initio","level":2,"score":0.4795803129673004},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.47354358434677124},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.47129762172698975},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.46318650245666504},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.37174805998802185},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34868931770324707},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.25682997703552246},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.13341552019119263},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1296217143535614},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1225791871547699},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.07934194803237915},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","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},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"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":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720008003783","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720008003783","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:18942163","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18942163","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W117625367","https://openalex.org/W1821638548","https://openalex.org/W1828921065","https://openalex.org/W1994983243","https://openalex.org/W2015470526","https://openalex.org/W2046192291","https://openalex.org/W2100063856","https://openalex.org/W2141915739","https://openalex.org/W2144152753","https://openalex.org/W2152064613","https://openalex.org/W2158714788","https://openalex.org/W2161151688","https://openalex.org/W2163822209","https://openalex.org/W2168211076","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2378076731","https://openalex.org/W4286888643","https://openalex.org/W3210795196","https://openalex.org/W2088988140","https://openalex.org/W2803103875","https://openalex.org/W2103019253","https://openalex.org/W2012531322","https://openalex.org/W2951529875","https://openalex.org/W2391453316","https://openalex.org/W2297768894"],"abstract_inverted_index":{"Protein":[0],"topology":[1],"representations":[2],"such":[3,72],"as":[4,73,125],"residue":[5],"contact":[6,26,39,94,102,192],"maps":[7,27,50,103,113,159],"are":[8],"an":[9,115],"important":[10],"intermediate":[11],"step":[12],"towards":[13],"ab":[14,190],"initio":[15,191],"prediction":[16],"of":[17,23,33,37,64,77,88,117,137],"protein":[18,70],"structure,":[19],"but":[20,133],"the":[21,34,74,86,129,153,157,175],"problem":[22,87],"predicting":[24,101],"reliable":[25],"is":[28,42,123,161,180],"far":[29],"from":[30,143],"solved.":[31],"One":[32],"main":[35],"pitfalls":[36],"existing":[38],"map":[40,193],"predictors":[41],"that":[43,51,152],"they":[44],"generally":[45],"predict":[46,91],"unphysical":[47],"maps,":[48],"i.e.":[49],"cannot":[52],"be":[53,185],"embedded":[54],"into":[55],"three-dimensional":[56],"structures":[57],"or,":[58],"at":[59],"best,":[60],"violate":[61],"a":[62,80,105,135,146],"number":[63,76,136],"basic":[65],"constraints":[66],"observed":[67],"in":[68],"real":[69],"structures,":[71],"maximum":[75],"contacts":[78],"for":[79],"residue.":[81],"Here,":[82],"we":[83,150,167,177],"focus":[84],"on":[85,165],"learning":[89],"to":[90,187],"more":[92],"\"physical\"":[93],"maps.":[95],"We":[96],"do":[97],"so":[98],"by":[99,114],"first":[100],"through":[104],"traditional":[106],"system":[107],"(XXStout),":[108],"and":[109],"then":[110],"filtering":[111],"these":[112],"ensemble":[116],"artificial":[118],"neural":[119],"networks.":[120],"The":[121],"filter":[122,154],"provided":[124],"input":[126],"not":[127],"only":[128],"bare":[130],"predicted":[131,158],"map,":[132],"also":[134],"global":[138],"or":[139],"long-range":[140],"features":[141],"extracted":[142],"it.":[144],"In":[145],"rigorous":[147],"cross-validation":[148],"test,":[149],"show":[151],"greatly":[155],"improves":[156],"it":[160,183],"input.":[162],"CASP7":[163],"results,":[164],"which":[166],"report":[168],"here,":[169],"corroborate":[170],"this":[171],"finding.":[172],"Importantly,":[173],"since":[174],"approach":[176],"present":[178],"here":[179],"fully":[181],"modular,":[182],"may":[184],"beneficial":[186],"any":[188],"other":[189],"predictor.":[194]},"counts_by_year":[{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}