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Computational Biophysics and Bioinformatics

Professor Emil Alexov Group

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Journal Articles by Y. Peng


Y.-R. Lee, K. Khan, K. Armfield-Uhas, S. Srikanth, N. A. Thompson, M. Pardo, L. Yu, J. W. Norris, et al.
Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy
Nature communications, 11(1), 1-17, 2020
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Y. Peng, R. Kelle, C. Little, E. Michonova, K. G. Kornev, and E. Alexov
pH-dependent interactions of Apolipophorin-III with a lipid disk
Journal of Computational Biophysics and Chemistry, 1-12, 2020
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R. Aprigliano, S. Bradamante, B. Mihaljevic, W. Wang, S. L. F. Martin, D. L. Bordin, M. Bosshard, N. P. Montaldo, et al.
Increased p53 signaling impairs neural differentiation causing HUWE1-promoted intellectual disabilities
bioRxiv, 2020
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S. K. Panday, M. H. Shashikala, M. Koirala, S. Pahari, A. Chakvorty, Y. Peng, L. Li, Z. Jia, et al.
Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1. 0]
Living Journal of Computational Molecular Science, 1(2), 10841, 2019
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B. Wu, Y. Peng, J. Eggert, and E. Alexov
Novel Genetic Markers for Early Detection of Elevated Breast Cancer Risk in Women
International journal of molecular sciences, 20(19), 4828, 2019
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Y. Peng, Y. Yang, L. Li, Z. Jia, W. Cao, and E. Alexov
DFMD: fast and effective DelPhiForce steered molecular dynamics approach to model ligand approach toward a receptor: Application to spermine synthase enzyme
Frontiers in molecular biosciences, 6, 74, 2019
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C. Li, Z. Jia, A. Chakravorty, S. Pahari, Y. Peng, S. Basu, M. Koirala, S. K. Panday, et al.
DelPhi suite: New developments and review of functionalities
Journal of computational chemistry, 40(28), 2502-2508, 2019
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C. J. Spellicy, Y. Peng, L. Olewiler, S. S. Cathey, R. C. Rogers, D. Bartholomew, J. Johnson, E. Alexov, et al.
Three additional patients with EED-associated overgrowth: potential mutation hotspots identified?
Journal of human genetics, 64(6), 561-572, 2019
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B. Wu, Y. Peng, J. A. Eggert, and E. Alexov
Investigating the Effects of Missense Mutations in MSH2 Gene Associated with Lynch Syndrome
Biophysical Journal, 116(3), 192a, 2019
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Y. Peng, M. Koirala, and E. Alexov
Electrostatic Force Driven Molecular Dynamics Simulations
Biophysical Journal, 116(3), 290a, 2019
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Y. Peng, E. Alexov, and S. Basu
Structural perspective on revealing and altering molecular functions of genetic variants linked with diseases
International journal of molecular sciences, 20(3), 548, 2019
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Y. Peng, E. Alexov, and S. Basu
Structural Perspective on Revealing and Altering Molecular Mechanisms of Genetic Variants Linked with Diseases
2018
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N. Tajielyato, L. Li, Y. Peng, J. Alper, and E. Alexov
E-hooks provide guidance and a soft landing for the microtubule binding domain of dynein
Scientific reports, 8(1), 1-10, 2018
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A. Chakravorty, Z. Jia, Y. Peng, N. Tajielyato, L. Wang, and E. Alexov
Gaussian-based smooth dielectric function: a surface-free approach for modeling macromolecular binding in solvents
Frontiers in molecular biosciences, 5, 25, 2018
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Z. Jia, L. Li, Y. Peng, F. Ding, and E. Alexov
The capricious electrostatic force: Revealing the signaling pathway in integrin α 2-I domain
Journal of Theoretical and Computational Chemistry, 17(3), 1840001, 2018
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C. J. Spellicy, J. Norris, R. Bend, C. Bupp, P. Mester, T. Reynolds, J. Dean, Y. Peng, et al.
Key apoptotic genes APAF1 and CASP9 implicated in recurrent folate-resistant neural tube defects
European Journal of Human Genetics, 26(3), 420-427, 2018
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Y. Peng, R. Myers, W. Zhang, and E. Alexov
Computational investigation of the missense mutations in DHCR7 gene associated with Smith-Lemli-Opitz syndrome
International journal of molecular sciences, 19(1), 141, 2018
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Y. Peng, L. Sun, Z. Jia, L. Li, and E. Alexov
Predicting protein--DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver
Bioinformatics, 34(5), 779-786, 2018
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L. Li, Z. Jia, Y. Peng, S. Godar, I. Getov, S. Teng, J. Alper, and E. Alexov
Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations
Scientific reports, 7(1), 1-12, 2017
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Y. Peng and E. Alexov
Protein Conformational Disease: Visit the Facts at a Glance
eLS, 1-7, 2017
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L. Li, Z. Jia, Y. Peng, A. Chakravorty, L. Sun, and E. Alexov
DelPhiForce web server: electrostatic forces and energy calculations and visualization
Bioinformatics, 33(22), 3661-3663, 2017
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Y. Peng and E. Alexov
Computational investigation of proton transfer, p K a shifts and p H-optimum of protein--DNA and protein--RNA complexes
Proteins: Structure, Function, and Bioinformatics, 85(2), 282-295, 2017
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Y. Peng and E. Alexov
Cofactors-loaded quaternary structure of lysine-specific demethylase 5C (KDM5C) protein: Computational model
Proteins: Structure, Function, and Bioinformatics, 84(12), 1797-1809, 2016
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Y. Peng, J. Norris, C. Schwartz, and E. Alexov
Revealing the effects of missense mutations causing Snyder-Robinson syndrome on the stability and dimerization of spermine synthase
International journal of molecular sciences, 17(1), 77, 2016
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Y. Peng and E. Alexov
Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding
Proteins: Structure, Function, and Bioinformatics, 84(2), 232-239, 2016
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Y. Peng, J. Suryadi, Y. Yang, T. G. Kucukkal, W. Cao, and E. Alexov
Mutations in the KDM5C ARID domain and their plausible association with syndromic Claes-Jensen-Type disease
International journal of molecular sciences, 16(11), 27270-27287, 2015
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Conference Papers


Y. Peng and E. Alexov
Predicting binding free energy change caused by missense mutations in protein-DNA interactions using modified MM/PBSA method
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2017
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