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PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions

Ning Zhang, Yuting Chen, Feiyang Zhao, Qing Yang, Franco L. Simonetti, Minghui Li, Emil Alexov
2018 PLoS Computational Biology  
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  ...  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  ...  Panchenko for providing useful suggestions. Author Contributions Conceptualization: Minghui Li. Predicting the effects of missense mutations on protein-DNA interactions  ... 
doi:10.1371/journal.pcbi.1006615 pmid:30533007 pmcid:PMC6303081 fatcat:jgcdwpytabbb5etrzms776pqt4

Systematic comparison and prediction of the effects of missense mutations on protein-DNA and protein-RNA interactions

Yao Jiang, Hui-Fang Liu, Rong Liu, Anna R. Panchenko
2021 PLoS Computational Biology  
The binding affinities of protein-nucleic acid interactions could be altered due to missense mutations occurring in DNA- or RNA-binding proteins, therefore resulting in various diseases.  ...  Here, we demonstrated that these two classes of mutations could generate similar or different tendencies for binding free energy changes in terms of the properties of mutated residues.  ...  Missense mutations occurring in DNA-or RNA-binding proteins could alter the above determinants, therefore leading to changes in binding free energies [5, 6] .  ... 
doi:10.1371/journal.pcbi.1008951 pmid:33872313 fatcat:aiu7rthwirb3zptvfc4mftj46a

iPNHOT: a knowledge-based approach for identifying protein-nucleic acid interaction hot spots

Xiaolei Zhu, Ling Liu, Jingjing He, Ting Fang, Yi Xiong, Julie C. Mitchell
2020 BMC Bioinformatics  
In this study, by collecting data from a recently published database dbAMEPNI, we proposed a new model, iPNHOT, to predict hotspots on both protein-DNA and protein-RNA interfaces.  ...  Hot spots are a small set of residues that contribute most to the binding affinity of a protein-nucleic acid interaction.  ...  Authors' contributions Availability of data and materials The webserver is at http://zhulab.ahu.edu.cn/iPNHOT/. The two data sets used in this study are included in the Additional file 2.  ... 
doi:10.1186/s12859-020-03636-w pmid:32631222 fatcat:2bzag6ijije2vfnxmj6k4kzciu

Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1.0]

Shailesh Kumar Panday, Mihiri H.B. Shashikala, Mahesh Koirala, Swagata Pahari, Arghya Chakrvorty, Yunhui Peng, Lin Li, Zhe Jia, Chuan Li, Emil Alexov
2019 Living journal of computational molecular science  
SAAMBE The Single Amino Acid Mutation based change in Binding free Energy (SAAMBE) [35] web-server predicts the change of protein binding free energy due to a mutation.  ...  SAAFEC Single Amino Acid Folding free Energy Changes (SAAFEC) program [38] predicts the folding free energy changes due to missense mutation.  ...  DelPhiPKa DelPhiPKa [22] is a DelPhi based C++ program, which predicts the pKa's of ionizable and polar groups in proteins, DNA and RNAs.  ... 
doi:10.33011/livecoms.1.2.10841 fatcat:5t5rrwvutvhxjjjka2d4tubyga