The art and science of molecular docking
Molecular docking has become an essential part of a structural biologist's and medicinal
chemist's toolkits. Given a chemical compound and the three-dimensional structure of a …
chemist's toolkits. Given a chemical compound and the three-dimensional structure of a …
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 …
Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness
Computational techniques applied to drug discovery have gained considerable popularity
for their ability to filter potentially active drugs from inactive ones, reducing the time scale …
for their ability to filter potentially active drugs from inactive ones, reducing the time scale …
Machine-learned molecular mechanics force fields from large-scale quantum chemical data
The development of reliable and extensible molecular mechanics (MM) force fields—fast,
empirical models characterizing the potential energy surface of molecular systems—is …
empirical models characterizing the potential energy surface of molecular systems—is …
The open force field initiative: Open software and open science for molecular modeling
L Wang, PK Behara, MW Thompson… - The Journal of …, 2024 - ACS Publications
Force fields are a key component of physics-based molecular modeling, describing the
energies and forces in a molecular system as a function of the positions of the atoms and …
energies and forces in a molecular system as a function of the positions of the atoms and …
Development and comprehensive benchmark of a high-quality amber-consistent small molecule force field with broad chemical space coverage for molecular …
B Xue, Q Yang, Q Zhang, X Wan, D Fang… - Journal of Chemical …, 2023 - ACS Publications
Biomolecular simulations have become an essential tool in contemporary drug discovery,
and molecular mechanics force fields (FFs) constitute its cornerstone. Developing a high …
and molecular mechanics force fields (FFs) constitute its cornerstone. Developing a high …
A transferable double exponential potential for condensed phase simulations of small molecules
The Lennard–Jones potential is the most widely-used function for the description of non-
bonded interactions in transferable force fields for the condensed phase. This is not because …
bonded interactions in transferable force fields for the condensed phase. This is not because …
Distribution of bound conformations in conformational ensembles for X-ray ligands predicted by the ANI-2X machine learning potential
In this study, we systematically studied the energy distribution of bioactive conformations of
small molecular ligands in their conformational ensembles using ANI-2X, a machine …
small molecular ligands in their conformational ensembles using ANI-2X, a machine …
Drug aggregation of sparingly-soluble ionizable drugs: molecular dynamics simulations of papaverine and prostaglandin F2α
Aggregation in aqueous solution can have important implications on both the in vivo
exposure of a drug and its pharmaceutical manufacturability. However, the drug aggregates …
exposure of a drug and its pharmaceutical manufacturability. However, the drug aggregates …
Data-driven parametrization of molecular mechanics force fields for expansive chemical space coverage
A force field is a critical component in molecular dynamics simulations for computational
drug discovery. It must achieve high accuracy within the constraints of molecular …
drug discovery. It must achieve high accuracy within the constraints of molecular …