Thermodynamics and kinetics of drug-target binding by molecular simulation
Computational studies play an increasingly important role in chemistry and biophysics,
mainly thanks to improvements in hardware and algorithms. In drug discovery and …
mainly thanks to improvements in hardware and algorithms. In drug discovery and …
[HTML][HTML] Best practices for alchemical free energy calculations [article v1. 0]
Alchemical free energy calculations are a useful tool for predicting free energy differences
associated with the transfer of molecules from one environment to another. The hallmark of …
associated with the transfer of molecules from one environment to another. The hallmark of …
Alchemical binding free energy calculations in AMBER20: Advances and best practices for drug discovery
Predicting protein–ligand binding affinities and the associated thermodynamics of
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …
Accelerating AutoDock4 with GPUs and Gradient-Based Local Search
AutoDock4 is a widely used program for docking small molecules to macromolecular targets.
It describes ligand–receptor interactions using a physics-inspired scoring function that has …
It describes ligand–receptor interactions using a physics-inspired scoring function that has …
Large-scale assessment of binding free energy calculations in active drug discovery projects
Accurate ranking of compounds with regards to their binding affinity to a protein using
computational methods is of great interest to pharmaceutical research. Physics-based free …
computational methods is of great interest to pharmaceutical research. Physics-based free …
The emerging role of computational design in peptide macrocycle drug discovery
VK Mulligan - Expert Opinion on Drug Discovery, 2020 - Taylor & Francis
Drug discovery is a laborious process with rising cost per new drug. Peptide macrocycles
are promising therapeutics, though conformational flexibility can reduce target affinity and …
are promising therapeutics, though conformational flexibility can reduce target affinity and …
Accelerating autodock vina with gpus
AutoDock Vina is one of the most popular molecular docking tools. In the latest benchmark
CASF-2016 for comparative assessment of scoring functions, AutoDock Vina won the best …
CASF-2016 for comparative assessment of scoring functions, AutoDock Vina won the best …
ACES: optimized alchemically enhanced sampling
We present an alchemical enhanced sampling (ACES) method implemented in the GPU-
accelerated AMBER free energy MD engine. The methods hinges on the creation of an …
accelerated AMBER free energy MD engine. The methods hinges on the creation of an …
AMBER free energy tools: a new framework for the design of optimized alchemical transformation pathways
We develop a framework for the design of optimized alchemical transformation pathways in
free energy simulations using nonlinear mixing and a new functional form for so-called …
free energy simulations using nonlinear mixing and a new functional form for so-called …
Simple adjustment of intranucleotide base-phosphate interaction in the ol3 amber force field improves RNA simulations
Molecular dynamics (MD) simulations represent an established tool to study RNA
molecules. The outcome of MD studies depends, however, on the quality of the force field …
molecules. The outcome of MD studies depends, however, on the quality of the force field …