Protein Design Python Packages

pymol-remote

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

arpeggia

Calculation of interatomic interactions in molecular structures

graphein

Protein Graph Library

molforge

A forge for protein workflows. One Python script, every tool in your stack.

gcgc

An ML-feature processing library for biological sequences.

proteingym

Official repository for the ProteinGym benchmarks

tr-rosetta-pytorch

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

protein-design-tools

A library of tools for protein design

proteinnpt

Official code repository for the paper "ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers"

flexs

Fitness landscape exploration sandbox for biological sequence design.

progen-torch

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

pen-assemble

Programmable Enzyme Networks: automated pipeline for IS110-family bridge recombinase design and scoring

protstruc

Protein structure handling in Python made easy.

rstoolbox

Python Toolbox For Rosetta Silent Files Processing

ggrecomb

Design chimeric protein libraries with Golden Gate Assembly.

protlib-designer

Integer Linear Programming for Protein Library Design

pyrif

Using Rotamer Interaction Fields from RIFGen/Dock in python

protein-watermark

Injecting watermarks to protein sequences for privacy protection in biosecurity

schemarecomb

Design recombinant protein libraries for Golden Gate Assembly.

rif

Rotamer Interaction Field protein design library