Computational Biophysics and Bioinformatics

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
Cell Reports Medicine, 2, 100240, 2021
URL, DOI, RIS, BibTex

G. Li, S. Panday, Y. Peng, and E. Alexov
SAMPDI-3D: predicting the effects of protein and DNA mutations on protein-DNA interactions.
Bioinformatics (Oxford, England), 2021
RIS, BibTex

G. Li, S. Panday, Y. Peng, and E. Alexov
SAMPDI-3D: predicting the effects of protein and DNA mutations on protein–DNA interactions
Bioinformatics, 37(21), 3760-3765, 2021
RIS, BibTex

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
RIS, BibTex

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
RIS, BibTex

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
RIS, BibTex

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
RIS, BibTex

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
RIS, BibTex

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
RIS, BibTex

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
RIS, BibTex

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
RIS, BibTex

Y. Peng, M. Koirala, and E. Alexov
Electrostatic Force Driven Molecular Dynamics Simulations
Biophysical Journal, 116(3), 290a, 2019
RIS, BibTex

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
RIS, BibTex

Y. Peng, E. Alexov, and S. Basu
Structural Perspective on Revealing and Altering Molecular Mechanisms of Genetic Variants Linked with Diseases
2018
RIS, BibTex

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
RIS, BibTex

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
RIS, BibTex

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
RIS, BibTex

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
RIS, BibTex

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
RIS, BibTex

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
RIS, BibTex

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
RIS, BibTex

Y. Peng and E. Alexov
Protein Conformational Disease: Visit the Facts at a Glance
eLS, 1-7, 2017
RIS, BibTex

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
RIS, BibTex

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
RIS, BibTex

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
RIS, BibTex

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
RIS, BibTex

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
RIS, BibTex

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
RIS, BibTex

Computational Biophysics and Bioinformatics

Professor Emil Alexov Group

Journal Articles by Y. Peng

Conference Papers