{"id":"https://openalex.org/W3191108515","doi":"https://doi.org/10.1093/bioinformatics/btab567","title":"SAMPDI-3D: predicting the effects of protein and DNA mutations on protein\u2013DNA interactions","display_name":"SAMPDI-3D: predicting the effects of protein and DNA mutations on protein\u2013DNA interactions","publication_year":2021,"publication_date":"2021-07-31","ids":{"openalex":"https://openalex.org/W3191108515","doi":"https://doi.org/10.1093/bioinformatics/btab567","mag":"3191108515","pmid":"https://pubmed.ncbi.nlm.nih.gov/34343273"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab567","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab567","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10186157/pdf/btab567.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100357036","display_name":"Gen Li","orcid":"https://orcid.org/0000-0002-6862-5547"},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gen Li","raw_affiliation_strings":["Department of Physics and Astronomy, Clemson University , Clemson, SC 29634, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics and Astronomy, Clemson University , Clemson, SC 29634, USA","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015469857","display_name":"Shailesh Kumar Panday","orcid":"https://orcid.org/0000-0003-3099-8679"},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shailesh Kumar Panday","raw_affiliation_strings":["Department of Physics and Astronomy, Clemson University , Clemson, SC 29634, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics and Astronomy, Clemson University , Clemson, SC 29634, USA","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082796473","display_name":"Yunhui Peng","orcid":"https://orcid.org/0000-0001-9768-4127"},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yunhui Peng","raw_affiliation_strings":["Department of Physics and Astronomy, Clemson University , Clemson, SC 29634, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics and Astronomy, Clemson University , Clemson, SC 29634, USA","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075727451","display_name":"Emil Alexov","orcid":"https://orcid.org/0000-0001-5346-0156"},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Emil Alexov","raw_affiliation_strings":["Department of Physics and Astronomy, Clemson University , Clemson, SC 29634, USA"],"raw_orcid":"https://orcid.org/0000-0001-5346-0156","affiliations":[{"raw_affiliation_string":"Department of Physics and Astronomy, Clemson University , Clemson, SC 29634, USA","institution_ids":["https://openalex.org/I8078737"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5075727451"],"corresponding_institution_ids":["https://openalex.org/I8078737"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.2688,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.79484692,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"37","issue":"21","first_page":"3760","last_page":"3765"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.44929999113082886,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.44929999113082886,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.14569999277591705,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.0754999965429306,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.6263250708580017},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4823724329471588},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.4586063027381897},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.44415953755378723},{"id":"https://openalex.org/keywords/dna-binding-protein","display_name":"DNA-binding protein","score":0.43269839882850647},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4251026511192322},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4163894057273865},{"id":"https://openalex.org/keywords/protein-methods","display_name":"Protein methods","score":0.41154178977012634},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.34915363788604736},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.22316566109657288},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.08936077356338501}],"concepts":[{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.6263250708580017},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4823724329471588},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.4586063027381897},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.44415953755378723},{"id":"https://openalex.org/C94966510","wikidata":"https://www.wikidata.org/wiki/Q2252764","display_name":"DNA-binding protein","level":4,"score":0.43269839882850647},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4251026511192322},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4163894057273865},{"id":"https://openalex.org/C111364199","wikidata":"https://www.wikidata.org/wiki/Q2915896","display_name":"Protein methods","level":4,"score":0.41154178977012634},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.34915363788604736},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.22316566109657288},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.08936077356338501},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","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":"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":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab567","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab567","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34343273","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34343273","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10186157","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10186157","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10186157/pdf/btab567.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:10186157","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10186157","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10186157/pdf/btab567.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.7599999904632568,"id":"https://metadata.un.org/sdg/7"}],"awards":[{"id":"https://openalex.org/G3687978964","display_name":null,"funder_award_id":"P20 GM121342","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3811072321","display_name":null,"funder_award_id":"R01GM125639","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6742222185","display_name":null,"funder_award_id":"R01GM093937","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7158946910","display_name":null,"funder_award_id":"R01 GM093937","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7238198058","display_name":null,"funder_award_id":"R01 GM125639","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7696160159","display_name":null,"funder_award_id":"R35 GM151964","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7831941416","display_name":null,"funder_award_id":"P20GM121342","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3191108515.pdf","grobid_xml":"https://content.openalex.org/works/W3191108515.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W54990013","https://openalex.org/W761483293","https://openalex.org/W1678356000","https://openalex.org/W1721232948","https://openalex.org/W1979447111","https://openalex.org/W1992977539","https://openalex.org/W1994122295","https://openalex.org/W2008708467","https://openalex.org/W2009254401","https://openalex.org/W2012627860","https://openalex.org/W2026690931","https://openalex.org/W2078040293","https://openalex.org/W2080085249","https://openalex.org/W2099672241","https://openalex.org/W2112702439","https://openalex.org/W2119137031","https://openalex.org/W2137221887","https://openalex.org/W2146217734","https://openalex.org/W2155844132","https://openalex.org/W2161910692","https://openalex.org/W2167296922","https://openalex.org/W2277931613","https://openalex.org/W2468620763","https://openalex.org/W2587481461","https://openalex.org/W2605361745","https://openalex.org/W2765235107","https://openalex.org/W2766808155","https://openalex.org/W2798552692","https://openalex.org/W2799593901","https://openalex.org/W2802867685","https://openalex.org/W2904602199","https://openalex.org/W2986863949","https://openalex.org/W2986886534","https://openalex.org/W2991016899","https://openalex.org/W3005188734","https://openalex.org/W3012929814","https://openalex.org/W3015602557","https://openalex.org/W3028007077","https://openalex.org/W3046740957","https://openalex.org/W3082121129","https://openalex.org/W3094281091","https://openalex.org/W3119533938","https://openalex.org/W3122561409","https://openalex.org/W4251816070","https://openalex.org/W6637404493","https://openalex.org/W6645288061","https://openalex.org/W6751169789","https://openalex.org/W6751616604","https://openalex.org/W6769934900","https://openalex.org/W6778366675"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W4321353415","https://openalex.org/W2745001401","https://openalex.org/W2130974462","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W4246352526","https://openalex.org/W2121910908","https://openalex.org/W2022959425","https://openalex.org/W2054945984"],"abstract_inverted_index":{"MOTIVATION:":[0],"Mutations":[1],"that":[2,45,170],"alter":[3],"protein-DNA":[4,24,50,97],"interactions":[5],"may":[6],"be":[7],"pathogenic":[8],"and":[9,35,109,127,166,195],"cause":[10],"diseases.":[11],"Therefore,":[12],"it":[13,167,171],"is":[14,82,118,168,179,189],"extremely":[15],"important":[16],"to":[17,28,36,91,120,160],"quantify":[18],"the":[19,30,38,47,56,61,79,93,96,106,110,113,138,146],"effect":[20,62],"of":[21,33,40,49,63,77,95,112,125,137],"mutations":[22,54,65,103,144],"on":[23],"binding":[25,51,57,98,107,139,147],"free":[26,99,140],"energy":[27,100,141],"reveal":[29],"molecular":[31],"origin":[32],"diseases":[34],"assist":[37],"development":[39],"treatments.":[41],"Although":[42],"several":[43],"methods":[44],"predict":[46,92],"change":[48,94,136],"affinity":[52],"upon":[53],"in":[55,104,129,145],"protein":[58,108,148],"were":[59,158],"developed,":[60],"DNA":[64],"was":[66],"not":[67],"considered":[68],"yet.":[69],"RESULTS:":[70],"Here,":[71],"we":[72],"report":[73],"a":[74,83,130,192,196],"new":[75],"version":[76],"SAMPDI,":[78],"SAMPDI-3D,":[80],"which":[81],"gradient":[84],"boosting":[85],"decision":[86],"tree":[87],"machine":[88],"learning":[89],"method":[90,117,178],"caused":[101,142],"by":[102,143],"both":[105],"bases":[111],"corresponding":[114],"DNA.":[115],"The":[116,177],"shown":[119,169],"achieve":[121],"Pearson":[122],"correlation":[123],"coefficient":[124],"0.76":[126],"0.80":[128],"benchmarking":[131],"test":[132],"against":[133],"experimentally":[134],"determined":[135],"or":[149],"DNA,":[150],"respectively.":[151],"Furthermore,":[152],"three":[153],"datasets":[154],"collected":[155],"from":[156],"literature":[157],"used":[159],"do":[161],"blind":[162],"benchmark":[163],"for":[164,183],"SAMPDI-3D":[165],"outperforms":[172],"all":[173],"existing":[174],"state-of-the-art":[175],"methods.":[176],"very":[180],"fast":[181],"allowing":[182],"genome-scale":[184],"investigations.":[185],"AVAILABILITYAND":[186],"IMPLEMENTATION:":[187],"It":[188],"available":[190,205],"as":[191],"web":[193],"server":[194],"stand-code":[197],"at":[198,206],"http://compbio.clemson.edu/SAMPDI-3D/.":[199],"SUPPLEMENTARY":[200],"INFORMATION:":[201],"Supplementary":[202],"data":[203],"are":[204],"Bioinformatics":[207],"online.":[208]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":8}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
