Dynamic PDB datasets

A simple python3 application to stack and optionally align raw images to reduce noise

Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost p…

Essential input parameters required for replicating the results presented in the submitted manuscript.

Predict the structure of immune receptor proteins

OpenMM plugin to interface with PLUMED

Protein-Ligand Benchmark Dataset for Free Energy Calculations

The public versio

MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.

Simple protein-ligand complex simulation with OpenMM

Force Fields

Implicit Solvent Approach Based on Generalised Born and Transferable Graph Neural Networks for Molecular Dynamics Simulations

A curated list of repositories related to fluid dynamics.

Minimal interface between Psi4 and OpenMM that allows passing of molecular systems between each program. Additionally, some helpful tools are included such as spherical addition of solvent (because…

Implementation of MOFF force field. Please cite us at Latham, A; Zhang, B J. Chem. Theory Comput. 2021, 17, 3134. (https://pubs.acs.org/doi/abs/10.1021/acs.jctc.0c01220)

Open Drug Discovery Toolkit

Tutorials and data necessary to reproduce the results of publication Machine Learning Coarse-Grained Potentials of Protein Thermodynamics

Example to fit parameters and run CG simulations using TorchMD and Schnet

Training neural network potentials

End-To-End Molecular Dynamics (MD) Engine using PyTorch

AI-powered Virtual Screening

Force Distribution Analysis (FDA) for GROMACS

Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)

An MPI based parallel implementation of Autodock Vina

A parallel molecular docking program based on AutoDock Vina

Quantum Mechanical Bespoke Force Field Derivation Toolkit

A bundle of deep-learning packages for biomolecular structure prediction and design contributed to the Rosetta Commons

Making Protein folding accessible to all!

Diffusion models of protein structure; trigonometry and attention are all you need!