{"id":"https://openalex.org/W4406047183","doi":"https://doi.org/10.1109/tcbbio.2024.3515200","title":"ResaPred: A Deep Residual Network With Self-Attention to Predict Protein Flexibility","display_name":"ResaPred: A Deep Residual Network With Self-Attention to Predict Protein Flexibility","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4406047183","doi":"https://doi.org/10.1109/tcbbio.2024.3515200","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811220"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2024.3515200","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2024.3515200","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","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/A5054667546","display_name":"Wei Wang","orcid":"https://orcid.org/0000-0002-9616-1145"},"institutions":[{"id":"https://openalex.org/I75955062","display_name":"Henan Normal University","ror":"https://ror.org/00s13br28","country_code":"CN","type":"education","lineage":["https://openalex.org/I75955062"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wei Wang","raw_affiliation_strings":["College of computer and Information Engineering, Henan Normal University, Xinxiang, China","Key Laboratory of Artificial Intelligence and Personalized Learning in Education of Henan Province, Xinxiang, China"],"affiliations":[{"raw_affiliation_string":"College of computer and Information Engineering, Henan Normal University, Xinxiang, China","institution_ids":["https://openalex.org/I75955062"]},{"raw_affiliation_string":"Key Laboratory of Artificial Intelligence and Personalized Learning in Education of Henan Province, Xinxiang, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109675511","display_name":"Shitong Wan","orcid":null},"institutions":[{"id":"https://openalex.org/I75955062","display_name":"Henan Normal University","ror":"https://ror.org/00s13br28","country_code":"CN","type":"education","lineage":["https://openalex.org/I75955062"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shitong Wan","raw_affiliation_strings":["College of computer and Information Engineering, Henan Normal University, Xinxiang, China"],"affiliations":[{"raw_affiliation_string":"College of computer and Information Engineering, Henan Normal University, Xinxiang, China","institution_ids":["https://openalex.org/I75955062"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000394846","display_name":"Hu Jin","orcid":"https://orcid.org/0000-0002-3505-6843"},"institutions":[{"id":"https://openalex.org/I4575257","display_name":"Hanyang University","ror":"https://ror.org/046865y68","country_code":"KR","type":"education","lineage":["https://openalex.org/I4575257"]},{"id":"https://openalex.org/I75955062","display_name":"Henan Normal University","ror":"https://ror.org/00s13br28","country_code":"CN","type":"education","lineage":["https://openalex.org/I75955062"]}],"countries":["CN","KR"],"is_corresponding":false,"raw_author_name":"Hu Jin","raw_affiliation_strings":["College of computer and Information Engineering, Henan Normal University, Xinxiang, China","School of Electrical Engineering, Hanyang University, Ansan, South Korea"],"affiliations":[{"raw_affiliation_string":"College of computer and Information Engineering, Henan Normal University, Xinxiang, China","institution_ids":["https://openalex.org/I75955062"]},{"raw_affiliation_string":"School of Electrical Engineering, Hanyang University, Ansan, South Korea","institution_ids":["https://openalex.org/I4575257"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032176468","display_name":"Dong Liu","orcid":"https://orcid.org/0000-0003-4346-9565"},"institutions":[{"id":"https://openalex.org/I75955062","display_name":"Henan Normal University","ror":"https://ror.org/00s13br28","country_code":"CN","type":"education","lineage":["https://openalex.org/I75955062"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dong Liu","raw_affiliation_strings":["College of computer and Information Engineering, Henan Normal University, Xinxiang, China","Key Laboratory of Artificial Intelligence and Personalized Learning in Education of Henan Province, Xinxiang, China"],"affiliations":[{"raw_affiliation_string":"College of computer and Information Engineering, Henan Normal University, Xinxiang, China","institution_ids":["https://openalex.org/I75955062"]},{"raw_affiliation_string":"Key Laboratory of Artificial Intelligence and Personalized Learning in Education of Henan Province, Xinxiang, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100330908","display_name":"Hongjun Zhang","orcid":"https://orcid.org/0009-0009-2446-2115"},"institutions":[{"id":"https://openalex.org/I4210146051","display_name":"Anyang Institute of Technology","ror":"https://ror.org/03sd3t490","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210146051"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongjun Zhang","raw_affiliation_strings":["School of Computer Science and Technology, Anyang University, Anyang, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Anyang University, Anyang, China","institution_ids":["https://openalex.org/I4210146051"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101778323","display_name":"Yun Zhou","orcid":"https://orcid.org/0009-0001-2413-894X"},"institutions":[{"id":"https://openalex.org/I75955062","display_name":"Henan Normal University","ror":"https://ror.org/00s13br28","country_code":"CN","type":"education","lineage":["https://openalex.org/I75955062"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yun Zhou","raw_affiliation_strings":["College of computer and Information Engineering, Henan Normal University, Xinxiang, China"],"affiliations":[{"raw_affiliation_string":"College of computer and Information Engineering, Henan Normal University, Xinxiang, China","institution_ids":["https://openalex.org/I75955062"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026708856","display_name":"Xianfang Wang","orcid":"https://orcid.org/0000-0001-8355-1470"},"institutions":[{"id":"https://openalex.org/I4210114043","display_name":"Henan Institute of Technology","ror":"https://ror.org/024f5m737","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210114043"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xianfang Wang","raw_affiliation_strings":["College of Computer Science and Technology Engineering, Henan Institute of Technology, Xinxiang, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology Engineering, Henan Institute of Technology, Xinxiang, China","institution_ids":["https://openalex.org/I4210114043"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5054667546"],"corresponding_institution_ids":["https://openalex.org/I75955062"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00151932,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"1","first_page":"216","last_page":"227"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9984999895095825,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9961000084877014,"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/flexibility","display_name":"Flexibility (engineering)","score":0.7608818411827087},{"id":"https://openalex.org/keywords/residual","display_name":"Residual","score":0.7407287359237671},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6430274248123169},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5455791354179382},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.502068281173706},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4022194445133209},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.25511854887008667},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15297913551330566},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1138005256652832}],"concepts":[{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.7608818411827087},{"id":"https://openalex.org/C155512373","wikidata":"https://www.wikidata.org/wiki/Q287450","display_name":"Residual","level":2,"score":0.7407287359237671},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6430274248123169},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5455791354179382},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.502068281173706},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4022194445133209},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.25511854887008667},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15297913551330566},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1138005256652832},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2024.3515200","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2024.3515200","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811220","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811220","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":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2","score":0.41999998688697815}],"awards":[{"id":"https://openalex.org/G2722085389","display_name":null,"funder_award_id":"62072160","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3907687336","display_name":null,"funder_award_id":"62072157","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5918011310","display_name":null,"funder_award_id":"20224BAB202022","funder_id":"https://openalex.org/F4320322665","funder_display_name":"Natural Science Foundation of Jiangxi Province"},{"id":"https://openalex.org/G8276734155","display_name":null,"funder_award_id":"62062063","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322665","display_name":"Natural Science Foundation of Jiangxi Province","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W596647800","https://openalex.org/W1540442759","https://openalex.org/W1964499168","https://openalex.org/W1974645077","https://openalex.org/W1977496900","https://openalex.org/W1995828610","https://openalex.org/W2000671825","https://openalex.org/W2008708467","https://openalex.org/W2076022844","https://openalex.org/W2087202599","https://openalex.org/W2097356092","https://openalex.org/W2115802401","https://openalex.org/W2124707779","https://openalex.org/W2126103104","https://openalex.org/W2127921600","https://openalex.org/W2130479394","https://openalex.org/W2136166518","https://openalex.org/W2141803423","https://openalex.org/W2145397344","https://openalex.org/W2149653886","https://openalex.org/W2153153865","https://openalex.org/W2156809104","https://openalex.org/W2158714788","https://openalex.org/W2194775991","https://openalex.org/W2474204065","https://openalex.org/W2510477141","https://openalex.org/W2511778323","https://openalex.org/W2515574711","https://openalex.org/W2587966957","https://openalex.org/W2598774641","https://openalex.org/W2786477584","https://openalex.org/W2786582016","https://openalex.org/W2794368672","https://openalex.org/W2795104011","https://openalex.org/W2797396541","https://openalex.org/W2802190049","https://openalex.org/W2804135590","https://openalex.org/W2911872747","https://openalex.org/W2952916873","https://openalex.org/W2982699907","https://openalex.org/W2998499403","https://openalex.org/W3008039059","https://openalex.org/W3008419553","https://openalex.org/W3131975258","https://openalex.org/W3177828909","https://openalex.org/W4282941459","https://openalex.org/W4283372224","https://openalex.org/W4309706838","https://openalex.org/W4310055273","https://openalex.org/W4316126727","https://openalex.org/W4317661995","https://openalex.org/W4372311821","https://openalex.org/W4384929351","https://openalex.org/W4385245566","https://openalex.org/W4385576706","https://openalex.org/W4393233076","https://openalex.org/W4396721167","https://openalex.org/W4401844424"],"related_works":["https://openalex.org/W2731899572","https://openalex.org/W3215138031","https://openalex.org/W3009238340","https://openalex.org/W4360585206","https://openalex.org/W4321369474","https://openalex.org/W4285208911","https://openalex.org/W3082895349","https://openalex.org/W4213079790","https://openalex.org/W2248239756","https://openalex.org/W3086377361"],"abstract_inverted_index":{"Grasping":[0],"the":[1,24,134,157,179,186],"intrinsic":[2],"properties":[3],"of":[4,26,30,93,181,188],"protein":[5,15,27,50,160,189],"structure":[6,162],"is":[7,29,62],"crucial":[8],"for":[9],"comprehending":[10],"relevant":[11],"biological":[12],"mechanisms,":[13],"with":[14,97,166],"flexibility":[16,28,145,187],"standing":[17],"out":[18],"as":[19,53,175],"a":[20,39,63,69,75,120],"critical":[21],"aspect.":[22],"Therefore,":[23],"prediction":[25],"great":[31],"importance":[32],"in":[33,123,143,184],"understanding":[34],"molecular":[35],"mechanisms.":[36],"We":[37,130],"propose":[38],"deep":[40,65,81],"learning":[41],"method":[42,183],"named":[43],"ResaPred,":[44],"which":[45,78],"extracts":[46,80],"diverse":[47],"features":[48,83],"from":[49],"sequences,":[51],"such":[52],"secondary":[54,161],"structure,":[55],"torsion":[56],"angle,":[57],"solvent":[58,164],"accessibility,":[59],"etc.":[60],"ResaPred":[61],"novel":[64],"network":[66,117],"based":[67],"on":[68,133],"modified":[70,88],"1D":[71,89],"residual":[72,90],"module":[73,91],"and":[74,99,136,139,163],"self-attention":[76,113],"mechanism,":[77],"effectively":[79],"key":[82],"related":[84],"to":[85,106,147,155],"flexibility.":[86,167],"The":[87],"consists":[92],"three":[94],"convolution":[95],"layers,":[96],"batchnorm":[98],"relu":[100],"layers":[101],"added":[102],"after":[103],"each":[104],"layer":[105],"prevent":[107],"gradient":[108],"explosion":[109],"or":[110],"vanishing.":[111],"Incorporating":[112],"mechanisms":[114],"into":[115],"neural":[116],"architectures":[118],"introduces":[119],"significant":[121],"advantage":[122],"capturing":[124],"long-range":[125],"dependencies":[126],"within":[127],"sequential":[128],"data.":[129],"conduct":[131],"experiments":[132],"non-strict":[135],"strict":[137],"cases,":[138],"achieve":[140],"state-of-the-art":[141],"results":[142],"predicting":[144],"compared":[146],"existing":[148],"methods.":[149],"Furthermore,":[150],"we":[151,169],"extended":[152],"our":[153,182],"analysis":[154],"explore":[156],"correlation":[158],"between":[159],"accessibility":[165],"Finally,":[168],"used":[170],"two":[171],"important":[172],"viral":[173],"proteins":[174],"case":[176],"studies,":[177],"confirming":[178],"effectiveness":[180],"recognizing":[185],"structures.":[190]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}