{"id":"https://openalex.org/W2766808155","doi":"https://doi.org/10.1093/bioinformatics/btx698","title":"Predicting protein\u2013DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver","display_name":"Predicting protein\u2013DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver","publication_year":2017,"publication_date":"2017-10-27","ids":{"openalex":"https://openalex.org/W2766808155","doi":"https://doi.org/10.1093/bioinformatics/btx698","mag":"2766808155","pmid":"https://pubmed.ncbi.nlm.nih.gov/29091991"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx698","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx698","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/5/779/25458384/btx698.pdf","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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/5/779/25458384/btx698.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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, USA"],"affiliations":[{"raw_affiliation_string":"Department of Physics and Astronomy, Clemson University, Clemson SC, USA","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069265168","display_name":"Lexuan Sun","orcid":null},"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":"Lexuan Sun","raw_affiliation_strings":["Department of Physics and Astronomy, Clemson University, Clemson SC, USA"],"affiliations":[{"raw_affiliation_string":"Department of Physics and Astronomy, Clemson University, Clemson SC, USA","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103031754","display_name":"Zhe Jia","orcid":"https://orcid.org/0000-0001-7709-9692"},"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":"Zhe Jia","raw_affiliation_strings":["Department of Physics and Astronomy, Clemson University, Clemson SC, USA"],"affiliations":[{"raw_affiliation_string":"Department of Physics and Astronomy, Clemson University, Clemson SC, USA","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100412796","display_name":"Lin Li","orcid":"https://orcid.org/0000-0001-5005-1218"},"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":"Lin Li","raw_affiliation_strings":["Department of Physics and Astronomy, Clemson University, Clemson SC, USA"],"affiliations":[{"raw_affiliation_string":"Department of Physics and Astronomy, Clemson University, Clemson SC, 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, USA"],"affiliations":[{"raw_affiliation_string":"Department of Physics and Astronomy, Clemson University, Clemson SC, USA","institution_ids":["https://openalex.org/I8078737"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"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":2.9775,"has_fulltext":false,"cited_by_count":78,"citation_normalized_percentile":{"value":0.92259681,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"34","issue":"5","first_page":"779","last_page":"786"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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":0.9994000196456909,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9987000226974487,"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/dna","display_name":"DNA","score":0.6589899063110352},{"id":"https://openalex.org/keywords/missense-mutation","display_name":"Missense mutation","score":0.6091457009315491},{"id":"https://openalex.org/keywords/dna-replication","display_name":"DNA replication","score":0.6032564043998718},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.47694507241249084},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.458895206451416},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4484357237815857},{"id":"https://openalex.org/keywords/molecular-mechanics","display_name":"Molecular mechanics","score":0.44775858521461487},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.41967514157295227},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.41025295853614807},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3152347207069397},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.29608309268951416},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2827385663986206},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.2132175862789154},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.14312490820884705}],"concepts":[{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.6589899063110352},{"id":"https://openalex.org/C75563809","wikidata":"https://www.wikidata.org/wiki/Q2656896","display_name":"Missense mutation","level":4,"score":0.6091457009315491},{"id":"https://openalex.org/C73573662","wikidata":"https://www.wikidata.org/wiki/Q130996","display_name":"DNA replication","level":3,"score":0.6032564043998718},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.47694507241249084},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.458895206451416},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4484357237815857},{"id":"https://openalex.org/C25057246","wikidata":"https://www.wikidata.org/wiki/Q1344441","display_name":"Molecular mechanics","level":3,"score":0.44775858521461487},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.41967514157295227},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.41025295853614807},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3152347207069397},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.29608309268951416},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2827385663986206},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.2132175862789154},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.14312490820884705}],"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":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020125","descriptor_name":"Mutation, Missense","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020125","descriptor_name":"Mutation, Missense","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020125","descriptor_name":"Mutation, Missense","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btx698","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx698","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/5/779/25458384/btx698.pdf","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:29091991","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29091991","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:europepmc.org:5373154","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6048991","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6048991","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6048991","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx698","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx698","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/5/779/25458384/btx698.pdf","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"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.8500000238418579,"display_name":"Affordable and clean energy"}],"awards":[{"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"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2766808155.pdf","grobid_xml":"https://content.openalex.org/works/W2766808155.grobid-xml"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W769759530","https://openalex.org/W1503104790","https://openalex.org/W1823111029","https://openalex.org/W1965549841","https://openalex.org/W1968754848","https://openalex.org/W1974599488","https://openalex.org/W1978050358","https://openalex.org/W1979447111","https://openalex.org/W1981482769","https://openalex.org/W1988027147","https://openalex.org/W2003207468","https://openalex.org/W2007095477","https://openalex.org/W2011658408","https://openalex.org/W2012627860","https://openalex.org/W2022430866","https://openalex.org/W2023490488","https://openalex.org/W2029667189","https://openalex.org/W2039276157","https://openalex.org/W2055166643","https://openalex.org/W2060872117","https://openalex.org/W2061777334","https://openalex.org/W2070871842","https://openalex.org/W2073995192","https://openalex.org/W2074645168","https://openalex.org/W2076890216","https://openalex.org/W2077481354","https://openalex.org/W2081184407","https://openalex.org/W2098134392","https://openalex.org/W2098312592","https://openalex.org/W2099672241","https://openalex.org/W2103459989","https://openalex.org/W2104155471","https://openalex.org/W2107594198","https://openalex.org/W2117541321","https://openalex.org/W2121464976","https://openalex.org/W2124735489","https://openalex.org/W2137154596","https://openalex.org/W2142868265","https://openalex.org/W2143079801","https://openalex.org/W2150981663","https://openalex.org/W2155844132","https://openalex.org/W2157122545","https://openalex.org/W2161652323","https://openalex.org/W2166248605","https://openalex.org/W2166765429","https://openalex.org/W2192013059","https://openalex.org/W2329374371","https://openalex.org/W2345331290","https://openalex.org/W2565758845","https://openalex.org/W2605361745","https://openalex.org/W2623747081","https://openalex.org/W6656512323"],"related_works":["https://openalex.org/W3004443428","https://openalex.org/W2090630809","https://openalex.org/W2153650863","https://openalex.org/W4361004911","https://openalex.org/W4253991465","https://openalex.org/W4246050813","https://openalex.org/W4391641617","https://openalex.org/W2625862723","https://openalex.org/W2069150591","https://openalex.org/W4232163425"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":12},{"year":2019,"cited_by_count":12},{"year":2018,"cited_by_count":4}],"updated_date":"2026-02-27T16:54:17.756197","created_date":"2025-10-10T00:00:00"}
