Peng Y - Search Results

1

SAAMBE-MEM: a sequence-based method for predicting binding free energy change upon mutation in membrane protein-protein complexes.

Rimal P, Panday SK, Xu W, Peng Y, Alexov E. Rimal P, et al. Among authors: peng y. Bioinformatics. 2024 Sep 2;40(9):btae544. doi: 10.1093/bioinformatics/btae544. Bioinformatics. 2024. PMID: 39240325 Free PMC article.

2

DelPhiForce web server: electrostatic forces and energy calculations and visualization.

Li L, Jia Z, Peng Y, Chakravorty A, Sun L, Alexov E. Li L, et al. Among authors: peng y. Bioinformatics. 2017 Nov 15;33(22):3661-3663. doi: 10.1093/bioinformatics/btx495. Bioinformatics. 2017. PMID: 29036596 Free PMC article.

3

Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver.

Peng Y, Sun L, Jia Z, Li L, Alexov E. Peng Y, et al. Bioinformatics. 2018 Mar 1;34(5):779-786. doi: 10.1093/bioinformatics/btx698. Bioinformatics. 2018. PMID: 29091991 Free PMC article.

4

SAMPDI-3D: predicting the effects of protein and DNA mutations on protein-DNA interactions.

Li G, Panday SK, Peng Y, Alexov E. Li G, et al. Among authors: peng y. Bioinformatics. 2021 Nov 5;37(21):3760-3765. doi: 10.1093/bioinformatics/btab567. Bioinformatics. 2021. PMID: 34343273 Free PMC article.

5

Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding.

Peng Y, Alexov E. Peng Y, et al. Proteins. 2016 Feb;84(2):232-9. doi: 10.1002/prot.24968. Epub 2016 Jan 11. Proteins. 2016. PMID: 26650512 Free PMC article.

6

Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes.

Peng Y, Alexov E. Peng Y, et al. Proteins. 2017 Feb;85(2):282-295. doi: 10.1002/prot.25221. Epub 2017 Jan 5. Proteins. 2017. PMID: 27936518 Free PMC article.

7

Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases.

Peng Y, Alexov E, Basu S. Peng Y, et al. Int J Mol Sci. 2019 Jan 28;20(3):548. doi: 10.3390/ijms20030548. Int J Mol Sci. 2019. PMID: 30696058 Free PMC article. Review.

8

Cofactors-loaded quaternary structure of lysine-specific demethylase 5C (KDM5C) protein: Computational model.

Peng Y, Alexov E. Peng Y, et al. Proteins. 2016 Dec;84(12):1797-1809. doi: 10.1002/prot.25162. Epub 2016 Oct 1. Proteins. 2016. PMID: 27696497 Free PMC article.

9

Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents.

Chakravorty A, Jia Z, Peng Y, Tajielyato N, Wang L, Alexov E. Chakravorty A, et al. Among authors: peng y. Front Mol Biosci. 2018 Mar 27;5:25. doi: 10.3389/fmolb.2018.00025. eCollection 2018. Front Mol Biosci. 2018. PMID: 29637074 Free PMC article.

10

Deciphering principles of nucleosome interactions and impact of cancer-associated mutations from comprehensive interaction network analysis.

Xu W, Zhang H, Guo W, Jiang L, Zhao Y, Peng Y. Xu W, et al. Among authors: peng y. Brief Bioinform. 2024 Jan 22;25(2):bbad532. doi: 10.1093/bib/bbad532. Brief Bioinform. 2024. PMID: 38329268 Free PMC article.

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