Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

Epitope Prediction Pipeline and analysis tools built around AlphaFold 2

Foldseek enables fast and sensitive comparisons of large structure sets.

Baseline model for PPB-Affinity benchmark data

workflow used to prepare PPB-Affinity database

Protein Ligand INteraction Dataset and Evaluation Resource

Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.

Remote protein homology detection suite.

Kuhlman Lab Installation of AlphaFold3

Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more

✌🏻 Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures (NeurIPS 2022)

An unofficial re-implementation of DiffAb, a diffusion-based generative model for antigen-specific antibody design and optimization.

Official repository for the Boltz-1 biomolecular interaction model

Chai-1, SOTA model for biomolecular structure prediction

ML toolset for creating TED: The Encyclopedia of Domains

Code for running RFdiffusion

Official git repository for Biopython (originally converted from CVS)

Saprot: Protein Language Model with Structural Alphabet (AA+3Di)

A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files

A dependency-free cross-platform swiss army knife for PDB files.

Multiple Protein Structure Alignment at Scale with FoldMason

Package for processing and analyzing glycans and their role in biology.

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

Inference code for Bio-Inspired Antibody Language Model

Predict the structure of immune receptor proteins

User friendly and accurate binder design pipeline