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alphafold2rave

awesome-molecular-generation

Awesome papers related to generative molecular modeling and design.

deep-drug-coder

deep-molecular-optimization

Molecular optimization by capturing chemist’s intuition using the Seq2Seq with attention and the Transformer

deepprotacs

diffdock

Colab version of "DiffDock: : Diffusion Steps, Twists, and Turns for Molecular Docking"

diffdock-original

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

graphinvent

Graph neural networks for molecular design.

kinase_msm

set of scripts to analyze kinases

mdtraj

An open library for the analysis of molecular dynamics trajectories

mead

Macroscopic Electrostatics with Atomic Detail

mead_2.2.9

A copy of MEAD v. 2.2.9 (Macroscopic Electrostatics with Atomic Detail) by Donald Bashford (released by the author under GPL v.1)

ml_md_utility_codes

Different utility codes for MD and ML

msm

msms

Markov state models

neuralforcefield

Neural Network Force Field based on PyTorch

novana

Novana is a cheminformatics tool that allows decomposing molecules into their scaffolds and shapes.

openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

pocket2mol

Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets

protac-rl

protacability

pysmilesutils

Utilities for working with SMILES based encodings of molecules for deep learning (PyTorch oriented)

rave

Reweighted Autoencoded Variational Bayes for Enhanced Sampling (RAVE)

rmsd-nn

siamese-rnn-self-attention

Contains code for Siamese Recurrent Neural Network with Self-Attention for Bioactivity Prediction

smi2sdf

Conversion of SMILES to SDF files through RDKit

uni-fold

An open-source platform for developing protein models beyond AlphaFold.