Molecular dynamics simulations in drug discovery and pharmaceutical development
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …
development process. In this review, we give a broad overview of the current application …
Molecular dynamics simulation for all
SA Hollingsworth, RO Dror - Neuron, 2018 - cell.com
The impact of molecular dynamics (MD) simulations in molecular biology and drug discovery
has expanded dramatically in recent years. These simulations capture the behavior of …
has expanded dramatically in recent years. These simulations capture the behavior of …
OPLS4: Improving force field accuracy on challenging regimes of chemical space
We report on the development and validation of the OPLS4 force field. OPLS4 builds upon
our previous work with OPLS3e to improve model accuracy on challenging regimes of drug …
our previous work with OPLS3e to improve model accuracy on challenging regimes of drug …
Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir
The pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2), has become a global crisis. Replication of SARS …
syndrome coronavirus 2 (SARS-CoV-2), has become a global crisis. Replication of SARS …
OPLS3e: Extending force field coverage for drug-like small molecules
Building upon the OPLS3 force field we report on an enhanced model, OPLS3e, that further
extends its coverage of medicinally relevant chemical space by addressing limitations in …
extends its coverage of medicinally relevant chemical space by addressing limitations in …
Class I histone deacetylases (HDAC1–3) are histone lysine delactylases
C Moreno-Yruela, D Zhang, W Wei, M Bæk, W Liu… - Science …, 2022 - science.org
Lysine L-lactylation [K (L-la)] is a newly discovered histone mark stimulated under conditions
of high glycolysis, such as the Warburg effect. K (L-la) is associated with functions that are …
of high glycolysis, such as the Warburg effect. K (L-la) is associated with functions that are …
Boosting protein–ligand binding pose prediction and virtual screening based on residue–atom distance likelihood potential and graph transformer
The past few years have witnessed enormous progress toward applying machine learning
approaches to the development of protein–ligand scoring functions. However, the robust …
approaches to the development of protein–ligand scoring functions. However, the robust …
[HTML][HTML] Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease
C Shivanika, D Kumar, V Ragunathan… - … structure & dynamics, 2020 - ncbi.nlm.nih.gov
The study aims to evaluate the potency of two hundred natural antiviral phytocompounds
against the active site of the Severe Acquired Respiratory Syndrome-Coronavirus− 2 (SARS …
against the active site of the Severe Acquired Respiratory Syndrome-Coronavirus− 2 (SARS …
[HTML][HTML] A suite of tutorials for the WESTPA rare-events sampling software [Article v1. 0]
The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …
generating pathways and rate constants for rare events such as protein folding and protein …
Molecular dynamics simulations of ionic liquids and electrolytes using polarizable force fields
Many applications in chemistry, biology, and energy storage/conversion research rely on
molecular simulations to provide fundamental insight into structural and transport properties …
molecular simulations to provide fundamental insight into structural and transport properties …