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

equiformer-pytorch

Equiformer - SE3/E3 Graph Attention Transformer for Molecules and Proteins

refua-clinical

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

clawcures

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

tr-rosetta-pytorch

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

refua-mcp

MCP server for Refua design, data, clinical, wet-lab, benchmark, regulatory, and deployment workflows.

invariant-point-attention

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

refua

Unified drug discovery ML toolkit

frustration-gpu

Pure-PyTorch LAMMPS-AWSEM frustration analysis. 14-53x faster than frustrapy on a single GPU. Byte-comparable to frustratometeR.

refua-deploy

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

refua-data

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

intellifold

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

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

Triangle Multiplicative Module

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.