{"id":"https://openalex.org/W4285144941","doi":"https://doi.org/10.1109/access.2022.3176945","title":"Constraint Guided Neighbor Generation for Protein Structure Prediction","display_name":"Constraint Guided Neighbor Generation for Protein Structure Prediction","publication_year":2022,"publication_date":"2022-01-01","ids":{"openalex":"https://openalex.org/W4285144941","doi":"https://doi.org/10.1109/access.2022.3176945"},"language":"en","primary_location":{"id":"doi:10.1109/access.2022.3176945","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2022.3176945","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/6514899/09779707.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://ieeexplore.ieee.org/ielx7/6287639/6514899/09779707.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091105936","display_name":"Rianon Zaman","orcid":"https://orcid.org/0000-0003-0763-5634"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Rianon Zaman","raw_affiliation_strings":["School of Information and Communication Technology, Griffith University, Nathan, QLD, Australia"],"raw_orcid":"https://orcid.org/0000-0003-0763-5634","affiliations":[{"raw_affiliation_string":"School of Information and Communication Technology, Griffith University, Nathan, QLD, Australia","institution_ids":["https://openalex.org/I11701301"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086354302","display_name":"M. A. Hakim Newton","orcid":"https://orcid.org/0000-0001-5655-0683"},"institutions":[{"id":"https://openalex.org/I78757542","display_name":"University of Newcastle Australia","ror":"https://ror.org/00eae9z71","country_code":"AU","type":"education","lineage":["https://openalex.org/I78757542"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"M. A. Hakim Newton","raw_affiliation_strings":["School of Information and Physical Sciences, The University of Newcastle, Callaghan, NSW, Australia"],"raw_orcid":"https://orcid.org/0000-0001-5655-0683","affiliations":[{"raw_affiliation_string":"School of Information and Physical Sciences, The University of Newcastle, Callaghan, NSW, Australia","institution_ids":["https://openalex.org/I78757542"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037269180","display_name":"Fereshteh Mataeimoghadam","orcid":"https://orcid.org/0000-0002-7619-787X"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Fereshteh Mataeimoghadam","raw_affiliation_strings":["School of Information and Communication Technology, Griffith University, Nathan, QLD, Australia"],"raw_orcid":"https://orcid.org/0000-0002-7619-787X","affiliations":[{"raw_affiliation_string":"School of Information and Communication Technology, Griffith University, Nathan, QLD, Australia","institution_ids":["https://openalex.org/I11701301"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038675407","display_name":"Abdul Sattar","orcid":"https://orcid.org/0000-0002-2567-2052"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Abdul Sattar","raw_affiliation_strings":["School of Information and Communication Technology, Griffith University, Nathan, QLD, Australia","School of Information and Communication Technology, Griffith University, Australia and Institute for Integrated and Intelligent Systems, Griffith University, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Communication Technology, Griffith University, Nathan, QLD, Australia","institution_ids":["https://openalex.org/I11701301"]},{"raw_affiliation_string":"School of Information and Communication Technology, Griffith University, Australia and Institute for Integrated and Intelligent Systems, Griffith University, Australia","institution_ids":["https://openalex.org/I11701301"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5091105936"],"corresponding_institution_ids":["https://openalex.org/I11701301"],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850},"fwci":0.4571,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.6547154,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"10","issue":null,"first_page":"54991","last_page":"55001"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9983000159263611,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9843999743461609,"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":0.7318775653839111},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6297154426574707},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5988690257072449},{"id":"https://openalex.org/keywords/generality","display_name":"Generality","score":0.5627200603485107},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5544636249542236},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.5055656433105469},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.49880051612854004},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.45349228382110596},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.43450722098350525},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3717910647392273},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32795411348342896},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.23670640587806702},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15298381447792053}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7318775653839111},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6297154426574707},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5988690257072449},{"id":"https://openalex.org/C2780767217","wikidata":"https://www.wikidata.org/wiki/Q5532421","display_name":"Generality","level":2,"score":0.5627200603485107},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5544636249542236},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.5055656433105469},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.49880051612854004},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.45349228382110596},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.43450722098350525},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3717910647392273},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32795411348342896},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.23670640587806702},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15298381447792053},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"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},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","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},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1109/access.2022.3176945","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2022.3176945","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/6514899/09779707.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:1737238298914f98adcf5a601b182615","is_oa":true,"landing_page_url":"https://doaj.org/article/1737238298914f98adcf5a601b182615","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Access, Vol 10, Pp 54991-55001 (2022)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/28999061","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"Journal contribution"},{"id":"pmh:oai:research-repository.griffith.edu.au:10072/418187","is_oa":true,"landing_page_url":"http://hdl.handle.net/10072/418187","pdf_url":null,"source":{"id":"https://openalex.org/S4306402548","display_name":"Griffith Research Online (Griffith University, Queensland, Australia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I11701301","host_organization_name":"Griffith University","host_organization_lineage":["https://openalex.org/I11701301"],"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":"","raw_type":"Journal article"},{"id":"pmh:uon:51069","is_oa":true,"landing_page_url":"http://hdl.handle.net/1959.13/1483006","pdf_url":null,"source":{"id":"https://openalex.org/S4377196471","display_name":"NOVA (University of Newcastle Australia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I78757542","host_organization_name":"University of Newcastle Australia","host_organization_lineage":["https://openalex.org/I78757542"],"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":"","raw_type":"journal article"}],"best_oa_location":{"id":"doi:10.1109/access.2022.3176945","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2022.3176945","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/6514899/09779707.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4526071058","display_name":null,"funder_award_id":"DP180102727","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"}],"funders":[{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4285144941.pdf","grobid_xml":"https://content.openalex.org/works/W4285144941.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W30464726","https://openalex.org/W59526888","https://openalex.org/W1988695007","https://openalex.org/W2004377868","https://openalex.org/W2008708467","https://openalex.org/W2104467962","https://openalex.org/W2117451312","https://openalex.org/W2126729622","https://openalex.org/W2131474431","https://openalex.org/W2132262459","https://openalex.org/W2145991251","https://openalex.org/W2157437977","https://openalex.org/W2158714788","https://openalex.org/W2171559274","https://openalex.org/W2345242111","https://openalex.org/W2540069603","https://openalex.org/W2622769796","https://openalex.org/W2765742208","https://openalex.org/W2767332469","https://openalex.org/W2769882797","https://openalex.org/W2772524698","https://openalex.org/W2778001245","https://openalex.org/W2791167534","https://openalex.org/W2808950571","https://openalex.org/W2905446269","https://openalex.org/W2949867299","https://openalex.org/W2951621517","https://openalex.org/W2951639995","https://openalex.org/W2967606876","https://openalex.org/W2970515102","https://openalex.org/W2994958577","https://openalex.org/W2997234557","https://openalex.org/W2999044305","https://openalex.org/W3012297767","https://openalex.org/W3035913543","https://openalex.org/W3048060386","https://openalex.org/W3106449773","https://openalex.org/W3109624714","https://openalex.org/W3177828909","https://openalex.org/W3209492740","https://openalex.org/W4237910213","https://openalex.org/W6603241369","https://openalex.org/W6844572246"],"related_works":["https://openalex.org/W2045049461","https://openalex.org/W1978893398","https://openalex.org/W2201908702","https://openalex.org/W4381094582","https://openalex.org/W2369625323","https://openalex.org/W2364579609","https://openalex.org/W1977906818","https://openalex.org/W1522139108","https://openalex.org/W2166914737","https://openalex.org/W4250855161"],"abstract_inverted_index":{"Protein":[0],"structure":[1],"prediction":[2],"(PSP)":[3],"is":[4],"essential":[5],"for":[6,53,108],"drug":[7],"discovery.":[8],"PSP":[9,21,54,95,183],"involves":[10],"minimising":[11],"an":[12,17,157],"unknown":[13],"scoring":[14,57,193],"function":[15,194],"over":[16],"astronomical":[18],"search":[19,51,79,102,167,184],"space.":[20],"has":[22],"achieved":[23],"significant":[24,172],"progress":[25],"recently":[26],"via":[27],"end-to-end":[28],"deep":[29,64],"learning":[30,65,69],"models":[31,70],"that":[32,186],"require":[33],"enormous":[34],"computational":[35],"resources":[36],"and":[37,73,111,138,204],"almost":[38],"all":[39],"known":[40],"proteins":[41,200],"as":[42,169],"training":[43],"data.":[44],"In":[45],"this":[46],"paper,":[47],"we":[48],"develop":[49],"conformational":[50,78,92,101],"methods":[52,80],"based":[55],"on":[56,115,195],"functions":[58],"involving":[59],"geometric":[60,124],"constraints":[61],"learnt":[62],"by":[63],"models.":[66],"When":[67],"machine":[68],"achieve":[71],"generality":[72],"thus":[74,112],"obviously":[75],"loose":[76],"accuracy,":[77],"could":[81,210],"perform":[82],"protein-specific":[83],"fine":[84],"tuning":[85],"of":[86,131,198,201],"the":[87,129,132,141],"predicted":[88],"conformations.":[89,147,177],"However,":[90],"effective":[91],"sampling":[93,189],"in":[94,213],"remains":[96],"a":[97,119,191,196],"key":[98],"challenge.":[99],"Existing":[100],"algorithms":[103,185],"adopt":[104],"random":[105,154,188],"selection":[106],"approaches":[107],"neighbor":[109],"generation":[110,208],"greatly":[113],"depend":[114],"luck.":[116],"We":[117],"propose":[118],"new":[120],"approach":[121,149,179,209],"to":[122,127,139,144,153],"analyse":[123],"constraint-based":[125],"scores,":[126,137],"identify":[128],"regions":[130,143],"current":[133],"conformations":[134],"causing":[135],"inferior":[136],"alter":[140],"identified":[142],"generate":[145],"neighbour":[146],"Our":[148,178,206],"prefers":[150],"informed":[151],"decisions":[152],"selections":[155],"from":[156,174],"artificial":[158],"intelligence":[159],"perspective.":[160],"The":[161],"proposed":[162],"method":[163],"also":[164],"provides":[165],"promising":[166],"guidance":[168],"it":[170],"obtains":[171],"improvements":[173],"given":[175],"initial":[176],"significantly":[180],"outperforms":[181],"state-of-the-art":[182],"use":[187],"with":[190],"similar":[192],"set":[197],"benchmark":[199],"varying":[202],"types":[203],"sizes.":[205],"sample":[207],"be":[211],"used":[212],"other":[214],"bioinformatics":[215],"research":[216],"areas":[217],"requiring":[218],"search.":[219]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
