Insights into protein–ligand interactions: mechanisms, models, and methods

X Du, Y Li, YL Xia, SM Ai, J Liang, P Sang… - International journal of …, 2016 - mdpi.com
Molecular recognition, which is the process of biological macromolecules interacting with
each other or various small molecules with a high specificity and affinity to form a specific …

Latest developments in molecular docking: 2010–2011 in review

E Yuriev, PA Ramsland - Journal of Molecular Recognition, 2013 - Wiley Online Library
The aim of docking is to accurately predict the structure of a ligand within the constraints of a
receptor binding site and to correctly estimate the strength of binding. We discuss, in detail …

DOCK 6: Impact of new features and current docking performance

WJ Allen, TE Balius, S Mukherjee… - Journal of …, 2015 - Wiley Online Library
This manuscript presents the latest algorithmic and methodological developments to the
structure‐based design program DOCK 6.7 focused on an updated internal energy function …

How molecular size impacts RMSD applications in molecular dynamics simulations

K Sargsyan, C Grauffel, C Lim - Journal of chemical theory and …, 2017 - ACS Publications
The root-mean-square deviation (RMSD) is a similarity measure widely used in analysis of
macromolecular structures and dynamics. As increasingly larger macromolecular systems …

Fatty acid-binding proteins (FABPs) are intracellular carriers for Δ9-tetrahydrocannabinol (THC) and cannabidiol (CBD)

MW Elmes, M Kaczocha, WT Berger, KN Leung… - Journal of Biological …, 2015 - ASBMB
Δ 9-Tetrahydrocannabinol (THC) and cannabidiol (CBD) occur naturally in marijuana
(Cannabis) and may be formulated, individually or in combination in pharmaceuticals such …

Fluoroquinolone Residues in the Environment Rapidly Induce Heritable Fluoroquinolone Resistance in Escherichia coli

H Liang, J Zhang, J Hu, X Li, B Li - Environmental Science & …, 2023 - ACS Publications
Extensive antibiotic use increases the environmental presence of their residues and may
accelerate the development of antibiotic resistance, although this remains poorly understood …

Cordycepin prevents radiation ulcer by inhibiting cell senescence via NRF2 and AMPK in rodents

Z Wang, Z Chen, Z Jiang, P Luo, L Liu, Y Huang… - Nature …, 2019 - nature.com
The pathological mechanisms of radiation ulcer remain unsolved and there is currently no
effective medicine. Here, we demonstrate that persistent DNA damage foci and cell …

A review on parallel virtual screening softwares for high-performance computers

NA Murugan, A Podobas, D Gadioli, E Vitali… - Pharmaceuticals, 2022 - mdpi.com
Drug discovery is the most expensive, time-demanding, and challenging project in
biopharmaceutical companies which aims at the identification and optimization of lead …

Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms

J Kirchmair, MJ Williamson, JD Tyzack… - Journal of chemical …, 2012 - ACS Publications
Metabolism of xenobiotics remains a central challenge for the discovery and development of
drugs, cosmetics, nutritional supplements, and agrochemicals. Metabolic transformations …

Destabilization of strigolactone receptor DWARF14 by binding of ligand and E3-ligase signaling effector DWARF3

LH Zhao, XE Zhou, W Yi, Z Wu, Y Liu, Y Kang, L Hou… - Cell research, 2015 - nature.com
Strigolactones (SLs) are endogenous hormones and exuded signaling molecules in plant
responses to low levels of mineral nutrients. Key mediators of the SL signaling pathway in …