{"id":"https://openalex.org/W4394892342","doi":"https://doi.org/10.1021/acs.jcim.4c00036","title":"Protein Engineering with Lightweight Graph Denoising Neural Networks","display_name":"Protein Engineering with Lightweight Graph Denoising Neural Networks","publication_year":2024,"publication_date":"2024-04-17","ids":{"openalex":"https://openalex.org/W4394892342","doi":"https://doi.org/10.1021/acs.jcim.4c00036","pmid":"https://pubmed.ncbi.nlm.nih.gov/38630581"},"language":"en","primary_location":{"is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00036","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.1101/2023.11.05.565665","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027695625","display_name":"Bingxin Zhou","orcid":"https://orcid.org/0000-0002-3897-9766"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bingxin Zhou","raw_affiliation_strings":["Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China","Shanghai National Center for Applied Mathematics (SJTU Center), Shanghai 200240, China"],"affiliations":[{"raw_affiliation_string":"Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Shanghai National Center for Applied Mathematics (SJTU Center), Shanghai 200240, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065268874","display_name":"Lirong Zheng","orcid":"https://orcid.org/0000-0001-6803-5048"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Lirong Zheng","raw_affiliation_strings":["Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China"],"affiliations":[{"raw_affiliation_string":"Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062998225","display_name":"Banghao Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Banghao Wu","raw_affiliation_strings":["Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China","School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China"],"affiliations":[{"raw_affiliation_string":"Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101964468","display_name":"Yang Tan","orcid":"https://orcid.org/0009-0004-7261-1705"},"institutions":[{"id":"https://openalex.org/I4391012619","display_name":"Shanghai Artificial Intelligence Laboratory","ror":"https://ror.org/03wkvpx79","country_code":null,"type":"facility","lineage":["https://openalex.org/I4391012619"]},{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]},{"id":"https://openalex.org/I4210100255","display_name":"Beijing Academy of Artificial Intelligence","ror":"https://ror.org/016a74861","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210100255"]},{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Tan","raw_affiliation_strings":["Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China","School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China","Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China"],"affiliations":[{"raw_affiliation_string":"Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China","institution_ids":["https://openalex.org/I4391012619","https://openalex.org/I4210100255"]},{"raw_affiliation_string":"School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China","institution_ids":["https://openalex.org/I143593769"]},{"raw_affiliation_string":"Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012900865","display_name":"Outongyi Lv","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Outongyi Lv","raw_affiliation_strings":["Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China"],"affiliations":[{"raw_affiliation_string":"Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100765686","display_name":"Kai Yi","orcid":"https://orcid.org/0000-0003-0415-3584"},"institutions":[{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Kai Yi","raw_affiliation_strings":["School of Mathematics and Statistics, University of New South Wales, Sydney 2052, Australia"],"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, University of New South Wales, Sydney 2052, Australia","institution_ids":["https://openalex.org/I31746571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034901082","display_name":"Guisheng Fan","orcid":"https://orcid.org/0000-0002-2702-0242"},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guisheng Fan","raw_affiliation_strings":["School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China","institution_ids":["https://openalex.org/I143593769"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000680377","display_name":"Liang Hong","orcid":"https://orcid.org/0000-0003-0107-336X"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210111959","display_name":"Shanghai Advanced Research Institute","ror":"https://ror.org/02br7py06","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210111959"]},{"id":"https://openalex.org/I4210100255","display_name":"Beijing Academy of Artificial Intelligence","ror":"https://ror.org/016a74861","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210100255"]},{"id":"https://openalex.org/I4391012619","display_name":"Shanghai Artificial Intelligence Laboratory","ror":"https://ror.org/03wkvpx79","country_code":null,"type":"facility","lineage":["https://openalex.org/I4391012619"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Liang Hong","raw_affiliation_strings":["Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China","Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China","Shanghai National Center for Applied Mathematics (SJTU Center), Shanghai 200240, China","Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 201203, China"],"affiliations":[{"raw_affiliation_string":"Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 201203, China","institution_ids":["https://openalex.org/I183067930","https://openalex.org/I4210111959"]},{"raw_affiliation_string":"Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Shanghai National Center for Applied Mathematics (SJTU Center), Shanghai 200240, China","institution_ids":[]},{"raw_affiliation_string":"Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China","institution_ids":["https://openalex.org/I4210100255","https://openalex.org/I4391012619"]}]}],"institution_assertions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5065268874","https://openalex.org/A5000680377"],"corresponding_institution_ids":["https://openalex.org/I183067930","https://openalex.org/I183067930","https://openalex.org/I4210111959","https://openalex.org/I4210100255","https://openalex.org/I4391012619"],"apc_list":null,"apc_paid":null,"fwci":6.985,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.999978,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"64","issue":"9","first_page":"3650","last_page":"3661"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.9967,"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/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.9967,"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":0.9893,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9882,"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":[],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6158074},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5460532},{"id":"https://openalex.org/C163294075","wikidata":"https://www.wikidata.org/wiki/Q581861","display_name":"Noise reduction","level":2,"score":0.5417119},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.48616645},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.47868901},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.39270455},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.22690392}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00036","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false},{"is_oa":true,"landing_page_url":"https://doi.org/10.1101/2023.11.05.565665","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory"],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38630581","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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1101/2023.11.05.565665","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory"],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false},"sustainable_development_goals":[],"grants":[{"funder":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China","award_id":"62302291"},{"funder":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China","award_id":"31630002"},{"funder":"https://openalex.org/F4320321881","funder_display_name":"Shanghai Municipal Education Commission","award_id":"2019-01-07-00-02-E00076"},{"funder":"https://openalex.org/F4320322999","funder_display_name":"Shanghai Jiao Tong University","award_id":null}],"datasets":[],"versions":[],"referenced_works_count":54,"referenced_works":["https://openalex.org/W1491063910","https://openalex.org/W1973253766","https://openalex.org/W1982289655","https://openalex.org/W1987054851","https://openalex.org/W2010356367","https://openalex.org/W2020356184","https://openalex.org/W2052478862","https://openalex.org/W2066015352","https://openalex.org/W2084262300","https://openalex.org/W2103132055","https://openalex.org/W2103496068","https://openalex.org/W2108962195","https://openalex.org/W2139414608","https://openalex.org/W2143210482","https://openalex.org/W2379594833","https://openalex.org/W2408615832","https://openalex.org/W2511213284","https://openalex.org/W2730472814","https://openalex.org/W2735621019","https://openalex.org/W2738980776","https://openalex.org/W2890223884","https://openalex.org/W2891927397","https://openalex.org/W2902293045","https://openalex.org/W2903887467","https://openalex.org/W2917580301","https://openalex.org/W2921718105","https://openalex.org/W2952700157","https://openalex.org/W2971780522","https://openalex.org/W2979417923","https://openalex.org/W2995514435","https://openalex.org/W3045075556","https://openalex.org/W3133458480","https://openalex.org/W3133917645","https://openalex.org/W3134185574","https://openalex.org/W3146944767","https://openalex.org/W3157999855","https://openalex.org/W3177500196","https://openalex.org/W3202848468","https://openalex.org/W3209435229","https://openalex.org/W3211728297","https://openalex.org/W4205773061","https://openalex.org/W4214886481","https://openalex.org/W4223581484","https://openalex.org/W4224988655","https://openalex.org/W4283698551","https://openalex.org/W4288067760","https://openalex.org/W4321369634","https://openalex.org/W4327550249","https://openalex.org/W4366520892","https://openalex.org/W4376121457","https://openalex.org/W4385802565","https://openalex.org/W4388024559","https://openalex.org/W4389279578","https://openalex.org/W4392807531"],"related_works":["https://openalex.org/W2391251536","https://openalex.org/W2375008505","https://openalex.org/W2362198218","https://openalex.org/W2350679292","https://openalex.org/W2085756966","https://openalex.org/W2042327336","https://openalex.org/W2033914206","https://openalex.org/W2019521278","https://openalex.org/W1984922432","https://openalex.org/W1982750869"],"abstract_inverted_index":{"Protein":[0],"engineering":[1],"faces":[2],"challenges":[3],"in":[4,50,156,180],"finding":[5],"optimal":[6],"mutants":[7,119,149],"from":[8],"a":[9,20,33,74,157,188],"massive":[10],"pool":[11],"of":[12,47,57,86,100,116,171],"candidate":[13],"mutants.":[14],"In":[15],"this":[16],"study,":[17],"we":[18],"introduce":[19],"deep-learning-based":[21],"data-efficient":[22],"fitness":[23],"prediction":[24],"tool":[25,190],"to":[26,66,141,152,176],"steer":[27],"protein":[28,40,181,192],"engineering.":[29,182],"Our":[30,88],"methodology":[31],"establishes":[32],"lightweight":[34],"graph":[35],"neural":[36],"network":[37],"scheme":[38],"for":[39,77,191],"structures,":[41],"which":[42],"efficiently":[43],"analyzes":[44],"the":[45,55,58,137,172,196],"microenvironment":[46],"amino":[48,59],"acids":[49],"wild-type":[51,122],"proteins":[52,79,127],"and":[53,109,128,146,198],"reconstructs":[54],"distribution":[56,71],"acid":[60],"sequences":[61],"that":[62],"are":[63,163],"more":[64],"likely":[65],"pass":[67],"natural":[68],"selection.":[69],"This":[70,166],"serves":[72],"as":[73,187],"general":[75],"guidance":[76],"scoring":[78],"toward":[80],"arbitrary":[81],"properties":[82,99,162],"on":[83],"any":[84],"order":[85],"mutations.":[87],"proposed":[89],"solution":[90],"undergoes":[91],"extensive":[92],"wet-lab":[93],"experimental":[94],"validation":[95],"spanning":[96],"diverse":[97],"physicochemical":[98,161],"various":[101],"proteins,":[102],"including":[103],"fluorescence":[104],"intensity,":[105],"antigen\u2013antibody":[106],"affinity,":[107],"thermostability,":[108],"DNA":[110],"cleavage":[111],"activity.":[112],"More":[113,131],"than":[114],"40%":[115],"ProtLGN-designed":[117],"single-site":[118],"outperform":[120],"their":[121],"counterparts":[123],"across":[124],"all":[125],"studied":[126],"targeted":[129],"properties.":[130],"importantly,":[132],"our":[133,184],"model":[134],"can":[135],"bypass":[136],"negative":[138],"epistatic":[139],"effect":[140],"combine":[142],"single":[143,158],"mutation":[144,154],"sites":[145,155],"form":[147],"deep":[148,178],"with":[150],"up":[151],"seven":[153],"round,":[159],"whose":[160],"significantly":[164],"improved.":[165],"observation":[167],"provides":[168],"compelling":[169],"evidence":[170],"structure-based":[173],"model's":[174],"potential":[175],"guide":[177],"mutations":[179],"Overall,":[183],"approach":[185],"emerges":[186],"versatile":[189],"engineering,":[193],"benefiting":[194],"both":[195],"computational":[197],"bioengineering":[199],"communities.":[200]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W4394892342","counts_by_year":[{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":1}],"updated_date":"2025-01-04T05:16:45.794420","created_date":"2024-04-18"}