Relative binding free energy calculations in drug discovery: recent advances and practical considerations
Accurate in silico prediction of protein–ligand binding affinities has been a primary objective
of structure-based drug design for decades due to the putative value it would bring to the …
of structure-based drug design for decades due to the putative value it would bring to the …
[HTML][HTML] Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS
The introduction of accelerator devices such as graphics processing units (GPUs) has had
profound impact on molecular dynamics simulations and has enabled order-of-magnitude …
profound impact on molecular dynamics simulations and has enabled order-of-magnitude …
Alchemical Free Energy Calculations on Membrane-Associated Proteins
Membrane proteins have diverse functions within cells and are well-established drug
targets. The advances in membrane protein structural biology have revealed drug and lipid …
targets. The advances in membrane protein structural biology have revealed drug and lipid …
Evolution of alchemical free energy methods in drug discovery
LF Song, KM Merz Jr - Journal of Chemical Information and …, 2020 - ACS Publications
The goal of the present manuscript is to succinctly trace the key technological steps in the
evolution of alchemical free energy methods (AFEMs) from a purely theoretical construct to a …
evolution of alchemical free energy methods (AFEMs) from a purely theoretical construct to a …
Toward fast and accurate binding affinity prediction with pmemdGTI: An efficient implementation of GPU-accelerated thermodynamic integration
We report the implementation of the thermodynamic integration method on the pmemd
module of the AMBER 16 package on GPUs (pmemdGTI). The pmemdGTI code typically …
module of the AMBER 16 package on GPUs (pmemdGTI). The pmemdGTI code typically …
Machine learning driven web-based app platform for the discovery of monoamine oxidase B inhibitors
Monoamine oxidases (MAOs), specifically MAO-A and MAO-B, play important roles in the
breakdown of monoamine neurotransmitters. Therefore, MAO inhibitors are crucial for …
breakdown of monoamine neurotransmitters. Therefore, MAO inhibitors are crucial for …
Boosting free-energy perturbation calculations with GPU-accelerated NAMD
Harnessing the power of graphics processing units (GPUs) to accelerate molecular
dynamics (MD) simulations in the context of free-energy calculations has been a …
dynamics (MD) simulations in the context of free-energy calculations has been a …
Accelerating drug discovery through tight integration of expert molecular design and predictive scoring
Highlights•Free energy calculations and computational solvent analysis guiding drug
discovery.•Drug discovery programs targeting acetyl-CoA carboxylase and tyrosine kinase …
discovery.•Drug discovery programs targeting acetyl-CoA carboxylase and tyrosine kinase …
Computational identification of potential inhibitors targeting cdk1 in colorectal cancer
Introduction: Despite improved treatment options, colorectal cancer (CRC) remains a huge
public health concern with a significant impact on affected individuals. Cell cycle …
public health concern with a significant impact on affected individuals. Cell cycle …
A GPU-accelerated parameter interpolation thermodynamic integration free energy method
TJ Giese, DM York - Journal of chemical theory and computation, 2018 - ACS Publications
There has been a resurgence of interest in free energy methods motivated by the
performance enhancements offered by molecular dynamics (MD) software written for …
performance enhancements offered by molecular dynamics (MD) software written for …