Rapid and reliable binding affinity prediction of bromodomain inhibitors: a computational study

S Wan, AP Bhati, SJ Zasada, I Wall… - Journal of chemical …, 2017 - ACS Publications
Binding free energies of bromodomain inhibitors are calculated with recently formulated
approaches, namely ESMACS (enhanced sampling of molecular dynamics with …

Computational studies of protein–drug binding affinity changes upon mutations in the drug target

R Friedman - Wiley Interdisciplinary Reviews: Computational …, 2022 - Wiley Online Library
Mutations that lead to drug resistance limit the efficacy of antibiotics, antiviral drugs, targeted
cancer therapies, and other treatments. Accurately calculating protein–drug binding affinity …

Investigating Multi-Target Antiviral Compounds by Screening of Phytochemicals From Neem (Azadirachta indica) Against PRRSV: A Vetinformatics Approach

RK Pathak, DY Kim, B Lim, JM Kim - Frontiers in Veterinary Science, 2022 - frontiersin.org
Porcine reproductive and respiratory syndrome virus (PRRSV) is a global health problem for
pigs. PRRSV is highly destructive and responsible for significant losses to the swine …

Impeccable: Integrated modeling pipeline for covid cure by assessing better leads

AA Saadi, D Alfe, Y Babuji, A Bhati, B Blaiszik… - Proceedings of the 50th …, 2021 - dl.acm.org
The drug discovery process currently employed in the pharmaceutical industry typically
requires about 10 years and $2–3 billion to deliver one new drug. This is both too expensive …

Global ranking of the sensitivity of interaction potential contributions within classical molecular dynamics force fields

W Edeling, M Vassaux, Y Yang, S Wan… - npj Computational …, 2024 - nature.com
Uncertainty quantification (UQ) is rapidly becoming a sine qua non for all forms of
computational science out of which actionable outcomes are anticipated. Much of the …

Novel linezolid-based oxazolidinones as potent anticandidiasis and antitubercular agents

S Faazil, MS Malik, SA Ahmed, RI Alsantali, P Yedla… - Bioorganic …, 2022 - Elsevier
The quest for new antifungal and antitubercular drugs is a need of the hour because of
morbid co-pathogenesis and an increase in immunocompromised patients. One of the ways …

Principles of small-molecule transport through synthetic nanopores

T Diederichs, K Ahmad, JR Burns, QH Nguyen… - ACS …, 2021 - ACS Publications
Synthetic nanopores made from DNA replicate the key biological processes of transporting
molecular cargo across lipid bilayers. Understanding transport across the confined lumen of …

Computational methods and theory for ion channel research

C Guardiani, F Cecconi, L Chiodo, G Cottone… - … in physics: X, 2022 - Taylor & Francis
Ion channels are fundamental biological devices that act as gates in order to ensure
selective ion transport across cellular membranes; their operation constitutes the molecular …

Long Time Scale Ensemble Methods in Molecular Dynamics: Ligand–Protein Interactions and Allostery in SARS-CoV-2 Targets

AP Bhati, A Hoti, A Potterton, MK Bieniek… - Journal of Chemical …, 2023 - ACS Publications
We subject a series of five protein–ligand systems which contain important SARS-CoV-2
targets, 3-chymotrypsin-like protease (3CLPro), papain-like protease, and adenosine ribose …

[HTML][HTML] Structural insight into the mechanisms and interacting features of endocrine disruptor Bisphenol A and its analogs with human estrogen-related receptor …

RK Pathak, JM Kim - Environmental Pollution, 2024 - Elsevier
Bisphenol A (BPA) is a very important chemical from the commercial perspective. Many
useful products are made from it, so its production is increasing day by day. It is widely …