DNA mismatches reveal conformational penalties in protein–DNA recognition

A Afek, H Shi, A Rangadurai, H Sahay, A Senitzki… - Nature, 2020 - nature.com
Transcription factors recognize specific genomic sequences to regulate complex gene-
expression programs. Although it is well-established that transcription factors bind to specific …

Computational approaches to prioritize cancer driver missense mutations

F Zhao, L Zheng, A Goncearenco… - International journal of …, 2018 - mdpi.com
Cancer is a complex disease that is driven by genetic alterations. There has been a rapid
development of genome-wide techniques during the last decade along with a significant …

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

Y Peng, L Sun, Z Jia, L Li, E Alexov - Bioinformatics, 2018 - academic.oup.com
Motivation Protein–DNA interactions are essential for regulating many cellular processes,
such as transcription, replication, recombination and translation. Amino acid mutations …

The pH effects on SARS-CoV and SARS-CoV-2 spike proteins in the process of binding to hACE2

Y **e, W Guo, A Lopez-Hernadez, S Teng, L Li - Pathogens, 2022 - mdpi.com
COVID-19 has been threatening human health since the late 2019, and has a significant
impact on human health and economy. Understanding SARS-CoV-2 and other …

Prediction of pKa values for neutral and basic drugs based on hybrid artificial intelligence methods

M Li, H Zhang, B Chen, Y Wu, L Guan - Scientific reports, 2018 - nature.com
The pKa value of drugs is an important parameter in drug design and pharmacology. In this
paper, an improved particle swarm optimization (PSO) algorithm was proposed based on …

PKAD-2: new entries and expansion of functionalities of the database of experimentally measured pKa's of proteins

N Ancona, A Bastola, E Alexov - Journal of computational biophysics …, 2023 - World Scientific
Almost all biological reactions are pH-dependent and understanding the origin of pH
dependence requires knowledge of the pKa's of ionizable groups. Here, we report a new …

A computational model to predict the structural and functional consequences of missense mutations in O6-methylguanine DNA methyltransferase

DT Kumar, E Mendonca, JP Christy, CGP Doss… - Advances in protein …, 2019 - Elsevier
DNA repair mechanism is a process through which the cell repairs its damaged DNA.
Although there are several mechanisms involved in the DNA repair mechanisms, the direct …

Electrostatic features for nucleocapsid proteins of SARS-CoV and SARS-CoV-2

W Guo, Y **e, AE Lopez-Hernandez… - Mathematical …, 2021 - pmc.ncbi.nlm.nih.gov
COVID-19 is increasingly affecting human health and global economy. Understanding the
fundamental mechanisms of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS …

Gaussian-based smooth dielectric function: a surface-free approach for modeling macromolecular binding in solvents

A Chakravorty, Z Jia, Y Peng, N Tajielyato… - Frontiers in molecular …, 2018 - frontiersin.org
Conventional modeling techniques to model macromolecular solvation and its effect on
binding in the framework of Poisson-Boltzmann based implicit solvent models make use of a …

Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein–DNA complexes, including the nucleosome

AV Onufriev - Frontiers in Molecular Biosciences, 2023 - frontiersin.org
Stability of a protein-ligand complex may be sensitive to pH of its environment. Here we
explore, computationally, stability of a set of protein-nucleic acid complexes using …