molecular-modeling

3dmol/3Dmol.js

WebGL accelerated JavaScript molecular graphics library

deepmodeling/Uni-Mol

Official Repository for the Uni-Mol Series Methods

gnina/gnina

A deep learning framework for molecular docking

isayev/ReLeaSE

Deep Reinforcement Learning for de-novo Drug Design

markovmodel/PyEMMA

🚂 Python API for Emma's Markov Model Algorithms 🚂

lukasturcani/stk

A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.

ClapeyronThermo/Clapeyron.jl

Clapeyron provides a framework for the development and use of fluid-thermodynamic models, including SAFT, cubic, activity, multi-parameter, and COSMO-SAC.

Acellera/moleculekit

MoleculeKit: Your favorite molecule manipulation kit

lsj2408/Transformer-M

[ICLR 2023] One Transformer Can Understand Both 2D & 3D Molecular Data (official implementation)

mojaie/MolecularGraph.jl

Graph-based molecule modeling toolkit for cheminformatics

AIRI-Institute/nablaDFT

nablaDFT: Large-Scale Conformational Energy and Hamiltonian Prediction benchmark and dataset

FermiQC/Fermi.jl

Fermi quantum chemistry program

TinkerTools/tinker

Tinker: Software Tools for Molecular Design

aiqm/aimnet

Atoms In Molecules Neural Network Potential

isayev/ANI1_dataset

A data set of 20 million calculated off-equilibrium conformations for organic molecules

swsoyee/r3dmol

🧬 An R package for visualizing molecular data in 3D

openmm/NNPOps

High-performance operations for neural network potentials

paiardin/DockingPie

A Consensus Docking Plugin for PyMOL

wlsong/PyLipID

A python toolkit for analysing membrane protein-lipid interactions.

alibaba/graph-gpt

Graph Learning with Generative Pretrained Transformers

tiejundong/FlexPose

FlexPose, a framework for AI-based flexible modeling of protein-ligand binding pose.

TinkerTools/tinker9

Tinker9: Next Generation of Tinker with GPU Support

HongxinXiang/ImageMol

ImageMol is a molecular image-based pre-training deep learning framework for computational drug discovery.

GMPavanLab/Swarm-CG

Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

Degiacomi-Lab/molearn

protein conformational spaces meet machine learning

smparker/molecular-blender

blend molecules!

aqlaboratory/pnerf

denoptim-project/DENOPTIM

DENOPTIM is a software package for de novo design and virtual screening of functional molecules of any kind.

yesint/pteros

Modern and fast molecular analysis and modeling library for C++ and Python

DrugBud-Suite/DockM8

All in one Structure-Based Virtual Screening workflow based on the concept of consensus docking.

bowman-lab/enspara

Modeling molecular ensembles with scalable data structures and parallel computing

lukasturcani/stk-vis

A cross-platform application for visualization of molecular databases.

20171130/Equivariant-NN-Zoo

A library for building equivariant neural networks and a zoo of implementations & examples.

qusers/Q6

Q6 Repository -- EVB, FEP and LIE simulator.

choderalab/gimlet

Graph Inference on MoLEcular Topology