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neuralplexer

NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

nnp-mm

Scripts to interface TorchANI NNP with NAMD

numpyro

Probabilistic programming with NumPy powered by JAX for autograd and JIT compilation to GPU/TPU/CPU.

openchem

OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

openforcefield

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

openmm-tensorrt

OpenMM plugin to define forces with a TensorRT graph

openmm-torch

OpenMM plugin to define forces with neural networks

openmm-tutorial-msbs

OpenMM tutorial for the MSBS course

openmm_sdm_workflow

Example of the use of the single-decoupling method setup workflow

openpathsampling

An open source Python framework for transition interface and path sampling calculations.

optimol

Optimization of binding affinities in chemical space for drug discovery

ord-schema

Schema for the Open Reaction Database

pdb2pqr-feedstock

A conda-smithy repository for pdb2pqr.

perses

Experiments with expanded ensembles to explore chemical space

physical_validation

Physical validation of molecular simulations

physical_validation_workshop

Python notebooks working though the physical_validation package

pipelines

Containerised components for cheminformatics and computational chemistry

pocket2mol

Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets

polaris

path of least action analysis on energy landscapes

poltype2

Poltype 2: Automated Parameterization and Free Energy Prediction for AMOEBA

propka-3.1

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

propka-feedstock

A conda-smithy repository for propka.

protocaller-1

Full automation of relative protein-ligand binding free energy calculations in GROMACS

psi4

Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python

psi4numpy

Combining Psi4 and Numpy for education and development.

pyautofep

PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods

pycharmm-workshop

pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the University of Michigan by Charles Brooks' Group, June 20-24.

pycontact

Analysis of non-covalent interactions in MD trajectories

pyemma-workshop

pyemma_tutorials

How to analyze molecular dynamics data with PyEMMA