Protein Design Python Packages

pymol-remote

Send data to and from pymol from a remote server (e.g. a cluster running deep learning workflows)

graphein

Protein Graph Library

arpeggia

A library for analyzing protein-protein interactions in PDB and mmCIF files

gcgc

GCGC is a preprocessing library for biological sequence model development.

tr-rosetta-pytorch

Implementation of trRosetta and trDesign for Pytorch, made into a convenient package, for protein structure prediction and design

flexs

FLEXS: an open simulation environment for developing and comparing model-guided biological sequence design algorithms.

protein-design-tools

A toolkit for protein structure analysis and design.

progen-torch

Implementation of the model from "ProGen: Language Modeling for Protein Generation"

proteingym

Official repository for the ProteinGym benchmarks

proteinnpt

ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers

rstoolbox

Python Toolbox For Rosetta Silent Files Processing

protstruc

Utility library for handling protein structures in Python.

protlib-designer

Integer Linear Programming for Protein Library Design

ggrecomb

Design chimeric protein libraries with Golden Gate Assembly.

pyrif

Using Rotamer Interaction Fields from RIFGen/Dock in python

schemarecomb

Design recombinant protein libraries for Golden Gate Assembly.

protein-watermark

Injecting watermarks to protein sequences for privacy protection in biosecurity

rif

Rotamer Interaction Field Python Libraries for Computational Protein Design