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abdockgen

acpype

OFFICIAL: AnteChamber PYthon Parser interfacE

alphafold

Open source code for AlphaFold.

alphafold_non_docker

autodock-vina

AutoDock Vina

deeplearning

深度学习入门教程, 优秀文章, Deep Learning Tutorial

diffsbdd

A Euclidean diffusion model for structure-based drug design.

drugex

Deep learning toolkit for Drug Design with Pareto-based Multi-Objective optimization in Polypharmacology

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

evoef

a fast and accurate physical energy function for predicting protein stability and protein-protein affinity changes upon amino-acid mutations

evoef2

a fast and accurate physical energy function extended from EvoEF for protein sequence design

faspr

an ultra-fast and accurate program for deterministic protein sidechain packing

gmx_mmpbsa

gmx_MMPBSA is a new tool aid to perform end-state free energy calculations based on AMBER's MMPBSA.py with GROMACS files.

localcolabfold

ColabFold on your local PC

macfrag

machine-learning-for-proteins

Listing of papers about machine learning for proteins.

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.

papers_for_protein_design_using_dl

List of papers about Proteins Design using Deep Learning

parallelfold

Modified version of Alphafold to divide CPU part (MSA and template searching) and GPU part. This can accelerate Alphafold when predicting multiple structures

peptide_design

This repository contains code for the paper: "Tertiary motifs as building blocks for the design of protein-binding peptides"

plmc

Inference of couplings in proteins and RNAs from sequence variation

pocket2mol

Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets

prottrans

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

pymol-open-source

Open-source foundation of the user-sponsored PyMOL molecular visualization system.

respre

ResPRE is an algorithm for protein residue-residue contact-map prediction

rifdock

Rifdock Library for Conformational Search

rosettafold

This package contains deep learning models and related scripts for RoseTTAFold

rosettafold-all-atom

signalp-6.0

Multi-class signal peptide prediction and structure decoding model.