{"id":"https://openalex.org/W4403743002","doi":"https://doi.org/10.2174/0109298665335283241003092139","title":"The Present State and Impact of AI-Driven Computational Tools for Predicting Plant Protein Structures","display_name":"The Present State and Impact of AI-Driven Computational Tools for Predicting Plant Protein Structures","publication_year":2024,"publication_date":"2024-10-24","ids":{"openalex":"https://openalex.org/W4403743002","doi":"https://doi.org/10.2174/0109298665335283241003092139","pmid":"https://pubmed.ncbi.nlm.nih.gov/39444187"},"language":"en","primary_location":{"id":"doi:10.2174/0109298665335283241003092139","doi":"https://doi.org/10.2174/0109298665335283241003092139","is_oa":false,"landing_page_url":"https://doi.org/10.2174/0109298665335283241003092139","pdf_url":null,"source":{"id":"https://openalex.org/S3577691","display_name":"Protein and Peptide Letters","issn_l":"0929-8665","issn":["0929-8665","1875-5305"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","jufo-1","ki-jl-1","medline","norway-1","poland-40","russia-white-list-3","vabb-shw"],"host_organization":"https://openalex.org/P4310320079","host_organization_name":"Bentham Science Publishers","host_organization_lineage":["https://openalex.org/P4310320079"],"host_organization_lineage_names":["Bentham Science Publishers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Protein & Peptide Letters","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"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/A5029574968","display_name":"Stanislaus Antony Ceasar","orcid":"https://orcid.org/0000-0003-4106-1531","observed_orcids":["https://orcid.org/0000-0003-4106-1531"]},"institutions":[{"id":"https://openalex.org/I4388891759","display_name":"Rajagiri College of Social Sciences (Autonomous)","ror":"https://ror.org/00tqx3b24","country_code":"IN","type":"education","lineage":["https://openalex.org/I4388891759"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Stanislaus Antony Ceasar","raw_affiliation_strings":["Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin - 683 104, Kerala, India"],"raw_orcid":"https://orcid.org/0000-0003-4106-1531","affiliations":[{"raw_affiliation_string":"Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin - 683 104, Kerala, India","institution_ids":["https://openalex.org/I4388891759"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079105322","display_name":"Heba Talat Ebeed","orcid":"https://orcid.org/0000-0002-3928-8123","observed_orcids":["https://orcid.org/0000-0002-3928-8123"]},"institutions":[{"id":"https://openalex.org/I126427551","display_name":"Damietta University","ror":"https://ror.org/035h3r191","country_code":"EG","type":"education","lineage":["https://openalex.org/I126427551"]},{"id":"https://openalex.org/I4210118384","display_name":"Academy of Scientific Research and Technology","ror":"https://ror.org/02k284p70","country_code":"EG","type":"nonprofit","lineage":["https://openalex.org/I4210118384"]}],"countries":["EG"],"is_corresponding":true,"raw_author_name":"Heba Talat Ebeed","raw_affiliation_strings":["Botany and Microbiology Department, Faculty of Science, Damietta\nUniversity, Damietta, Egypt","National Biotechnology Network of Expertise (NBNE), Academy of Scientific Research and Technology (ASRT), Cairo, Egypt","Botany and Microbiology Department, Faculty of Science, Damietta University, Egypt"],"raw_orcid":"https://orcid.org/0000-0002-3928-8123","affiliations":[{"raw_affiliation_string":"Botany and Microbiology Department, Faculty of Science, Damietta\nUniversity, Damietta, Egypt","institution_ids":["https://openalex.org/I126427551"]},{"raw_affiliation_string":"National Biotechnology Network of Expertise (NBNE), Academy of Scientific Research and Technology (ASRT), Cairo, Egypt","institution_ids":["https://openalex.org/I4210118384"]},{"raw_affiliation_string":"Botany and Microbiology Department, Faculty of Science, Damietta University, Egypt","institution_ids":["https://openalex.org/I126427551"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5079105322"],"corresponding_institution_ids":["https://openalex.org/I126427551","https://openalex.org/I4210118384"],"apc_list":null,"apc_paid":null,"fwci":0.7588,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.63327374,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"31","issue":"10","first_page":"749","last_page":"758"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9765999913215637,"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":0.9765999913215637,"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":0.013799999840557575,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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":0.007400000002235174,"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/alphafold","display_name":"AlphaFold","score":0.8939999938011169},{"id":"https://openalex.org/keywords/plant-proteomics","display_name":"plant proteomics","score":0.7459999918937683},{"id":"https://openalex.org/keywords/crops","display_name":"cultivated plants","score":0.8230000138282776},{"id":"https://openalex.org/keywords/arabidopsis-thaliana","display_name":"Arabidopsis thaliana","score":0.972000002861023},{"id":"https://openalex.org/keywords/soybean","display_name":"soybean","score":0.9449999928474426},{"id":"https://openalex.org/keywords/protein-structure-determination","display_name":"protein structure determination","score":0.5120000243186951},{"id":"https://openalex.org/keywords/protein-engineering","display_name":"protein engineering","score":0.5239999890327454},{"id":"https://openalex.org/keywords/agronomic-traits","display_name":"agronomic traits","score":0.7379999756813049}],"concepts":[{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.6525766253471375},{"id":"https://openalex.org/C137580998","wikidata":"https://www.wikidata.org/wiki/Q235352","display_name":"Crop","level":2,"score":0.5474309921264648},{"id":"https://openalex.org/C3019009989","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Plant protein","level":2,"score":0.5075591802597046},{"id":"https://openalex.org/C2775988993","wikidata":"https://www.wikidata.org/wiki/Q158695","display_name":"Arabidopsis thaliana","level":4,"score":0.4983053207397461},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4915960729122162},{"id":"https://openalex.org/C132215390","wikidata":"https://www.wikidata.org/wiki/Q461335","display_name":"Abiotic component","level":2,"score":0.48199716210365295},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.4655728042125702},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.45162928104400635},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3918658494949341},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3377978205680847},{"id":"https://openalex.org/C150903083","wikidata":"https://www.wikidata.org/wiki/Q7108","display_name":"Biotechnology","level":1,"score":0.3306891918182373},{"id":"https://openalex.org/C6557445","wikidata":"https://www.wikidata.org/wiki/Q173113","display_name":"Agronomy","level":1,"score":0.3092854619026184},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.13968214392662048},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09827882051467896},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08012092113494873},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C31903555","wikidata":"https://www.wikidata.org/wiki/Q1637030","display_name":"Food science","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010940","descriptor_name":"Plant Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010940","descriptor_name":"Plant Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010940","descriptor_name":"Plant Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018556","descriptor_name":"Crops, Agricultural","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018556","descriptor_name":"Crops, Agricultural","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018556","descriptor_name":"Crops, Agricultural","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.2174/0109298665335283241003092139","doi":"https://doi.org/10.2174/0109298665335283241003092139","is_oa":false,"landing_page_url":"https://doi.org/10.2174/0109298665335283241003092139","pdf_url":null,"source":{"id":"https://openalex.org/S3577691","display_name":"Protein and Peptide Letters","issn_l":"0929-8665","issn":["0929-8665","1875-5305"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","jufo-1","ki-jl-1","medline","norway-1","poland-40","russia-white-list-3","vabb-shw"],"host_organization":"https://openalex.org/P4310320079","host_organization_name":"Bentham Science Publishers","host_organization_lineage":["https://openalex.org/P4310320079"],"host_organization_lineage_names":["Bentham Science Publishers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Protein & Peptide Letters","raw_type":"journal-article"},{"id":"pmid:39444187","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39444187","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,"listed_in":[],"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":"Protein and peptide letters","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2","score":0.991100013256073}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W1589711326","https://openalex.org/W1940906693","https://openalex.org/W1979590043","https://openalex.org/W2002151814","https://openalex.org/W2019632488","https://openalex.org/W2024135146","https://openalex.org/W2035477608","https://openalex.org/W2051210555","https://openalex.org/W2062693912","https://openalex.org/W2075684035","https://openalex.org/W2077592902","https://openalex.org/W2086953892","https://openalex.org/W2116496925","https://openalex.org/W2145268834","https://openalex.org/W2151831732","https://openalex.org/W2153335878","https://openalex.org/W2156233383","https://openalex.org/W2166199589","https://openalex.org/W2277331476","https://openalex.org/W2323907705","https://openalex.org/W2528327487","https://openalex.org/W2574496196","https://openalex.org/W2803476351","https://openalex.org/W2808337148","https://openalex.org/W2898210859","https://openalex.org/W2968494487","https://openalex.org/W2999044305","https://openalex.org/W3000017363","https://openalex.org/W3005800881","https://openalex.org/W3078287400","https://openalex.org/W3082773775","https://openalex.org/W3128285641","https://openalex.org/W3159328869","https://openalex.org/W3177828909","https://openalex.org/W3183366938","https://openalex.org/W3183475563","https://openalex.org/W3186179742","https://openalex.org/W3186934009","https://openalex.org/W3208626065","https://openalex.org/W3208999135","https://openalex.org/W3215498386","https://openalex.org/W4224304709","https://openalex.org/W4226027101","https://openalex.org/W4280548378","https://openalex.org/W4296239075","https://openalex.org/W4309153596","https://openalex.org/W4309506674","https://openalex.org/W4317661995","https://openalex.org/W4323309784","https://openalex.org/W4383187654","https://openalex.org/W4385662717","https://openalex.org/W4385898787","https://openalex.org/W4391656874","https://openalex.org/W4397023962","https://openalex.org/W4399770380","https://openalex.org/W4405106177"],"related_works":["https://openalex.org/W4412441007","https://openalex.org/W7203930890","https://openalex.org/W7163330902","https://openalex.org/W7140863179","https://openalex.org/W4412065675","https://openalex.org/W4409472572","https://openalex.org/W4410605122","https://openalex.org/W7139129731","https://openalex.org/W2921947057","https://openalex.org/W7204255929"],"abstract_inverted_index":{"Several":[0],"key":[1,47,88,218],"functions":[2],"of":[3,20,23,28,61,86,105,112,132,135,151,170,189,225],"plants,":[4],"such":[5],"as":[6],"photosynthesis,":[7],"nutrient":[8],"transport,":[9],"disease":[10],"resistance,":[11],"and":[12,30,43,66,121,178,202],"abiotic":[13],"tolerance,":[14],"are":[15,76],"manifested":[16],"by":[17],"several":[18,152],"classes":[19],"proteins.":[21],"Prediction":[22],"3-":[24],"dimensional":[25],"(3-D)":[26],"structures":[27,75,118],"proteins":[29,154],"their":[31,116],"working":[32],"mechanisms":[33],"can":[34],"have":[35,91,114,184],"a":[36,93,179,186],"profound":[37],"impact":[38],"on":[39],"plant":[40,62,82,127,207],"proteomics":[41],"research":[42],"could":[44],"help":[45,199],"improve":[46,221],"agricultural":[48],"traits":[49],"in":[50,109,206],"crop":[51,89,157,182,226],"plants.":[52,158,227],"This":[53],"review":[54],"aims":[55],"to":[56,216,220],"present":[57],"the":[58,68,80,87,106,110,125,129,166,204,222],"current":[59],"status":[60],"protein":[63,74,107,136,143,162,173],"structure":[64,144,208,212],"determination":[65,209],"discuss":[67],"way":[69],"forward.":[70],"Most":[71,85],"experimentally":[72,98,119,139],"proven":[73,99],"available":[77],"only":[78,92],"for":[79,155],"model":[81],"Arabidopsis":[83],"thaliana.":[84],"plants":[90,113,183],"few":[94,180],"hundred":[95],"or":[96],"fewer":[97],"3-D":[100],"structures.":[101,141],"Fewer":[102],"than":[103],"1%":[104],"sequences":[108,137,174,192],"majority":[111],"had":[115],"3D":[117],"determined,":[120],"A.":[122],"thaliana":[123],"is":[124],"sole":[126],"with":[128,138,175,193],"highest":[130,167],"percentage":[131,168,188],"1.4":[133],"%":[134],"determined":[140],"AI-based":[142],"prediction":[145],"tool":[146],"AlphaFold":[147,160,194,197],"has":[148,165],"predicted":[149,161,176,195],"models":[150,201],"thousand":[153],"many":[156],"In":[159],"models,":[163,177],"soybean":[164],"(65%)":[169],"its":[171,190],"UniProt":[172,191],"other":[181],"also":[185],"considerable":[187],"models.":[196],"might":[198,214],"predict":[200],"bridge":[203],"gap":[205],"studies.":[210],"Protein":[211],"information":[213],"lead":[215],"engineering":[217],"residues":[219],"agronomical":[223],"performance":[224]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2024-10-25T00:00:00"}