Protein Design Python Packages

pymol-remote

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

avitai-artifex

Generative modeling for JAX/Flax NNX: VAEs, GANs, DDPM/DDIM/score/DiT/latent diffusion, normalizing flows, energy-based, autoregressive and geometric (SE(3), protein, point cloud, mesh) models; image, text, audio, molecular, protein, tabular and time-series modalities; a shared Trainer with callbacks and extensions; evaluation through calibrax.

arpeggia

Calculation of interatomic interactions in molecular structures

graphein

Protein Graph Library

bionemo-ir

Easy, fast, and memory-efficient structure prediction inference

aminx

JAX/Equinox implementation of ProteinMPNN and LigandMPNN for protein sequence design

gcgc

An ML-feature processing library for biological sequences.

protein-design-tools

A library of tools for protein design

bindsight

Expression to Binder: joins cohort RNA-seq target discovery to de novo protein binder design in one reproducible workflow, with PROV-O/RO-Crate provenance from every ranked binder back to the patient samples.

molforge

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

proteingym

Official repository for the ProteinGym benchmarks

binderqc

QC and tag-site scoring for designed protein binders from predicted complexes.

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.

tr-rosetta-pytorch

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

protstruc

Protein structure handling in Python made easy.

pen-assemble

Automated design and scoring engine for IS110-family bridge recombinase variants, nominating 1,029 candidates via an 8-axis PenScore over pre-registered predictions.

rstoolbox

Python Toolbox For Rosetta Silent Files Processing

pyrif

Using Rotamer Interaction Fields from RIFGen/Dock in python

ggrecomb

Design chimeric protein libraries with Golden Gate Assembly.

protlib-designer

Design diverse, optimized protein libraries with multi-objective integer programming, deep mutational scanning, protein language models, and inverse folding.

progen-torch

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

protein-watermark

Injecting watermarks to protein sequences for privacy protection in biosecurity

schemarecomb

Design chimeric protein libraries with Golden Gate Assembly.