Enhanced sampling methods for molecular dynamics simulations
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …
molecular dynamics simulations and allow the sampling of larger portions of the …
Machine learning directed drug formulation development
Abstract Machine learning (ML) has enabled ground-breaking advances in the healthcare
and pharmaceutical sectors, from improvements in cancer diagnosis, to the identification of …
and pharmaceutical sectors, from improvements in cancer diagnosis, to the identification of …
Development and benchmarking of open force field 2.0. 0: the Sage small molecule force field
We introduce the Open Force Field (OpenFF) 2.0. 0 small molecule force field for drug-like
molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF …
molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF …
[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 …
Enhancing hit discovery in virtual screening through absolute protein–ligand binding free-energy calculations
In the hit identification stage of drug discovery, a diverse chemical space needs to be
explored to identify initial hits. Contrary to empirical scoring functions, absolute protein …
explored to identify initial hits. Contrary to empirical scoring functions, absolute protein …
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 …
Development and benchmarking of open force field v1. 0.0—the parsley small-molecule force field
We present a methodology for defining and optimizing a general force field for classical
molecular simulations, and we describe its use to derive the Open Force Field 1.0. 0 small …
molecular simulations, and we describe its use to derive the Open Force Field 1.0. 0 small …
GROMACS in the cloud: A global supercomputer to speed up alchemical drug design
C Kutzner, C Kniep, A Cherian… - Journal of Chemical …, 2022 - ACS Publications
We assess costs and efficiency of state-of-the-art high-performance cloud computing and
compare the results to traditional on-premises compute clusters. Our use case is atomistic …
compare the results to traditional on-premises compute clusters. Our use case is atomistic …
Large-scale assessment of binding free energy calculations in active drug discovery projects
CEM Schindler, H Baumann, A Blum… - Journal of Chemical …, 2020 - ACS Publications
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 …
Assessment of binding affinity via alchemical free-energy calculations
M Kuhn, S Firth-Clark, P Tosco, ASJS Mey… - Journal of Chemical …, 2020 - ACS Publications
Free-energy calculations have seen increased usage in structure-based drug design.
Despite the rising interest, automation of the complex calculations and subsequent analysis …
Despite the rising interest, automation of the complex calculations and subsequent analysis …