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openfold

Trainable 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.

opensmog

OpenSMOG is a Python library for performing molecular dynamics simulations using Structure-Based Models. OpenSMOG uses OpenMM.

optim

OptimLib: a lightweight C++ library of numerical optimization methods for nonlinear functions

prodigy

Repository containing various scripts to predict the binding affinity of protein-protein complexes from structure

protein-design-tutorials

Tutorials, cheat sheets, and other resources for computational methods for protein design.

proteinmpnn

Code for the ProteinMPNN paper

proteinnet

Standardized data set for machine learning of protein structure

pymol-script-repo

Collected scripts for Pymol

raptorx-3dmodeling

refinegnn

rosetta

rosettafold

This package contains deep learning models and related scripts for RoseTTAFold

rosettafold2na

RoseTTAFold2 protein/nucleic acid complex prediction

rosettasilenttoolbox

Python Toolbox For Rosetta Silent Files Processing

silent_tools

A bunch of shell utilities for dealing the silent files

symmol

SYMMOL: a program to find the maximum symmetry group in an atom cluster

tmalign

This repo is outdated. Please use https://github.com/pylelab/USalign instead

trdesign

trRosetta for protein design

trrosetta

A package to predict protein inter-residue geometries from sequence data

trrosetta2_training_set

weblogo

WebLogo 3: Sequence Logos redrawn