{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T22:57:04Z","timestamp":1772146624612,"version":"3.50.1"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2017,10,28]],"date-time":"2017-10-28T00:00:00Z","timestamp":1509148800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01GM093937"],"award-info":[{"award-number":["R01GM093937"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Protein\u2013DNA interactions are essential for regulating many cellular processes, such as transcription, replication, recombination and translation. Amino acid mutations occurring in DNA-binding proteins have profound effects on protein\u2013DNA binding and are linked with many diseases. Hence, accurate and fast predictions of the effects of mutations on protein\u2013DNA binding affinity are essential for understanding disease-causing mechanisms and guiding plausible treatments.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here we report a new method Single Amino acid Mutation binding free energy change of Protein\u2013DNA Interaction (SAMPDI). The method utilizes modified Molecular Mechanics Poisson-Boltzmann Surface Area (MM\/PBSA) approach along with an additional set of knowledge-based terms delivered from investigations of the physicochemical properties of protein\u2013DNA complexes. The method is benchmarked against experimentally determined binding free energy changes caused by 105 mutations in 13 proteins (compiled ProNIT database and data from recent references), and results in correlation coefficient of 0.72.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>http:\/\/compbio.clemson.edu\/SAMPDI<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx698","type":"journal-article","created":{"date-parts":[[2017,10,27]],"date-time":"2017-10-27T19:11:45Z","timestamp":1509131505000},"page":"779-786","source":"Crossref","is-referenced-by-count":69,"title":["Predicting protein\u2013DNA binding free energy change upon missense mutations using modified MM\/PBSA approach: SAMPDI webserver"],"prefix":"10.1093","volume":"34","author":[{"given":"Yunhui","family":"Peng","sequence":"first","affiliation":[{"name":"Department of Physics and Astronomy, Clemson University, Clemson SC, USA"}]},{"given":"Lexuan","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy, Clemson University, Clemson SC, USA"}]},{"given":"Zhe","family":"Jia","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy, Clemson University, Clemson SC, USA"}]},{"given":"Lin","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy, Clemson University, Clemson SC, USA"}]},{"given":"Emil","family":"Alexov","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy, Clemson University, Clemson SC, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,10,28]]},"reference":[{"key":"2023012712412158900_btx698-B1","doi-asserted-by":"crossref","first-page":"3257","DOI":"10.1021\/ct300400x","article-title":"Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone phi, psi and side-chain chi(1) and chi(2) dihedral angles","volume":"8","author":"Best","year":"2012","journal-title":"J. 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