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• W2904602199 endingPage "e1006615" @default.
• W2904602199 startingPage "e1006615" @default.
• W2904602199 abstract "Protein-DNA interactions play important roles in regulations of many vital cellular processes, including transcription, translation, DNA replication and recombination. Sequence variants occurring in these DNA binding proteins that alter protein-DNA interactions may cause significant perturbations or complete abolishment of function, potentially leading to diseases. Developing a mechanistic understanding of impacts of variants on protein-DNA interactions becomes a persistent need. To address this need we introduce a new computational method PremPDI that predicts the effect of single missense mutation in the protein on the protein-DNA interaction and calculates the quantitative binding affinity change. The PremPDI method is based on molecular mechanics force fields and fast side-chain optimization algorithms with parameters optimized on experimental sets of 219 mutations from 49 protein-DNA complexes. PremPDI yields a very good agreement between predicted and experimental values with Pearson correlation coefficient of 0.71 and root-mean-square error of 0.86 kcal mol-1. The PremPDI server could map mutations on a structural protein-DNA complex, calculate the associated changes in binding affinity, determine the deleterious effect of a mutation, and produce a mutant structural model for download. PremPDI can be applied to many tasks, such as determination of potential damaging mutations in cancer and other diseases. PremPDI is available at http://lilab.jysw.suda.edu.cn/research/PremPDI/." @default.
• W2904602199 created "2018-12-22" @default.
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• W2904602199 date "2018-12-11" @default.
• W2904602199 modified "2023-10-16" @default.
• W2904602199 title "PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions" @default.
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• W2904602199 doi "https://doi.org/10.1371/journal.pcbi.1006615" @default.
• W2904602199 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/6303081" @default.
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• W2904602199 hasPublicationYear "2018" @default.
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