End-point binding free energy calculation with MM/PBSA and MM/GBSA: strategies and applications in drug design

E Wang, H Sun, J Wang, Z Wang, H Liu… - Chemical …, 2019‏ - ACS Publications
Molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …

Molecular dynamics-driven drug discovery: lea** forward with confidence

A Ganesan, ML Coote, K Barakat - Drug discovery today, 2017‏ - Elsevier
Highlights•Currently, develo** a market-approved drug costs a staggering $2.6 billion.•In
silico methods have become an important strategy for narrowing down on promising lead …

Understanding the binding affinity of noscapines with protease of SARS-CoV-2 for COVID-19 using MD simulations at different temperatures

D Kumar, K Kumari, A Jayaraj, V Kumar… - Journal of …, 2021‏ - Taylor & Francis
The current outbreak of a novel coronavirus, named as SARS-CoV-2 causing COVID-19
occurred in 2019, is in dire need of finding potential therapeutic agents. Recently, ongoing …

[HTML][HTML] Oximes: Novel therapeutics with anticancer and anti-inflammatory potential

IA Schepetkin, MB Plotnikov, AI Khlebnikov… - Biomolecules, 2021‏ - mdpi.com
Oximes have been studied for decades because of their significant roles as
acetylcholinesterase reactivators. Over the last twenty years, a large number of oximes have …

Phosphorylation-driven epichaperome assembly is a regulator of cellular adaptability and proliferation

T Roychowdhury, SW McNutt, C Pasala… - Nature …, 2024‏ - nature.com
The intricate network of protein-chaperone interactions is crucial for maintaining cellular
function. Recent discoveries have unveiled the existence of specialized chaperone …

The normal-mode entropy in the MM/GBSA method: effect of system truncation, buffer region, and dielectric constant

S Genheden, O Kuhn, P Mikulskis… - Journal of chemical …, 2012‏ - ACS Publications
We have performed a systematic study of the entropy term in the MM/GBSA (molecular
mechanics combined with generalized Born and surface-area solvation) approach to …

Structure guided design of potent and selective ponatinib-based hybrid inhibitors for RIPK1

M Najjar, C Suebsuwong, SS Ray, RJ Thapa, JL Maki… - Cell reports, 2015‏ - cell.com
RIPK1 and RIPK3, two closely related RIPK family members, have emerged as important
regulators of pathologic cell death and inflammation. In the current work, we report that the …

MM-GB (PB) SA calculations of protein-ligand binding free energies

JM Hayes, G Archontis - Molecular dynamics-studies of synthetic …, 2012‏ - books.google.com
The importance of computational chemistry in modern scientific research is well established.
Continuous improvement in software and algorithms for the modeling of chemical …

Toward rational design of selective molecularly imprinted polymers (MIPs) for proteins: computational and experimental studies of acrylamide based polymers for …

MV Sullivan, SR Dennison, G Archontis… - The Journal of …, 2019‏ - ACS Publications
Molecularly imprinted polymers (MIPs) have potential as alternatives to antibodies in the
diagnosis and treatment of disease. However, atomistic level knowledge of the …

Adipocytes as anticancer drug delivery depot

D Wen, J Wang, G Van Den Driessche, Q Chen… - Matter, 2019‏ - cell.com
Tumor-associated adipocytes promote tumor growth by providing energy and causing
chronic inflammation. Here, we have exploited the lipid metabolism to engineer adipocytes …