Niu Huang's Lab

BindingNet

can-ai-do

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

generalization_benchmark

benchmark_DOCK_Vina

flexible-docking

Amber_beginning

db2mol2

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

fpdb

fetch PDB database information

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.

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

auto-dud-e

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

AutoDock-Vina

AutoDock Vina

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)

FreeSolv

Experimental and calculated small molecule hydration free energies

gnina

A deep learning framework for molecular docking

MetalDock

Dock organometallic compounds to proteins/DNA/biomolecules

oddt

Open Drug Discovery Toolkit

qvina

Accurately speed up AutoDock Vina