Protein Folding Python Packages

prospr

Prospr is a universal toolbox for protein structure prediction within the HP-model. The Python package is based on a C++ core, which gives Prospr its high performance. The C++ core is made available as a separate zip file to facilitate high-performance computing applications. The package comes with many prediction algorithms and datasets to use.

alphafold2-pytorch

To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released

molforge

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

equiformer-pytorch

Implementation of the Equiformer, SE3/E3 equivariant attention network that reaches new SOTA, and adopted for use by EquiFold for protein folding

intellifold

IntelliFold: A Controllable Foundation Model for General and Specialized Biomolecular Structure Prediction.

invariant-point-attention

Implementation of Invariant Point Attention, used for coordinate refinement in the structure module of Alphafold2, as a standalone Pytorch module

tr-rosetta-pytorch

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

clawcures

Campaign orchestration layer built on OpenClaw planning and refua-mcp execution.

refua-mcp

Model Context Protocol server exposing typed Refua tools for folding, affinity, design, and optional clinical and preclinical workflows.

refua

Python drug discovery toolkit for Boltz2 structure and affinity prediction, BoltzGen binder and antibody design, and TxGemma ADMET integration in one API.

refua-data

Data ingestion, caching, and parquet materialization for the Refua drug discovery ecosystem.

refua-clinical

PK/PD-driven virtual patient and clinical trial simulation toolkit for Refua.

frustration-gpu

Pure-PyTorch reimplementation of LAMMPS-AWSEM frustration analysis (Wolynes-lab AWSEM Hamiltonian + Ferreiro frustration index), GPU-accelerated.

refua-deploy

Deployment automation for Refua campaign workloads across private and public clouds.

refua-regulatory

Regulatory and audit evidence packaging for Refua campaign decisions.

refua-bench

Benchmark and regression gate tooling for Refua workflows.

refua-studio

Web control plane for Refua campaign orchestration and scientific execution.

triangle-multiplicative-module

Implementation of the Triangle Multiplicative module, used in Alphafold2 as an efficient way to mix rows or columns of a 2d feature map, as a standalone package for Pytorch

refua-wetlab

Unified API layer for wet lab automation across multiple providers.

hpsandbox

a package of Python modules and example scripts for experimenting with the two-dimensional HP lattice model of Dill and Chan.