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amber_beginning

auto-dud-e

Auto-DUD-E is a website for a test set of ligands & decoys for molecular docking.

autodock-vina

AutoDock Vina

benchmark_dock_vina

bindingnet

can-ai-do

Predicting or pretending: artificial intelligence for protein-ligand interactions lack of sufficiently large and unbiased datasets

db2mol2

Convert DB2 file back to Mol2. That could be useful in db2 development or other application.

deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics

dgl-lifesci

Python package for graph neural networks in chemistry and biology

dpdata

Manipulating DeePMD-kit, VASP, LAMMPS data formats.

dpgen

The deep potential generator

fast

Fusion models for Atomic and molecular STructures (FAST)

flexible-docking

fpdb

fetch PDB database information

freesolv

Experimental and calculated small molecule hydration free energies

generalization_benchmark

gnina

A deep learning framework for molecular docking

oddt

Open Drug Discovery Toolkit

openff-toolkit

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

pydock3

Python package wrapping the DOCK Fortran program and providing several tools built on top of it.

qvina

Accurately speed up AutoDock Vina

rdkit

The official sources for the RDKit library

teachopencadd

TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data

torsionnet

A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM

wyz_graduate_design_code

some scripts