Protein-protein interaction network constructed with STRING database

Data Munging for BioGRID data to form interaction networks for further processing.

A Motif Hash Based Method for Matching Crosslinkers into Peptides and Proteins

Chai-1, SOTA model for biomolecular structure prediction

Open source implementation of AlphaFold3

A scalable generative AI framework built for researchers and developers working on Large Language Models, Multimodal, and Speech AI (Automatic Speech Recognition and Text-to-Speech)

PINDER: The Protein INteraction Dataset and Evaluation Resource

A short course on proteins and protein design aimed at early career students

Protein Ligand INteraction Dataset and Evaluation Resource

Listing of papers about machine learning for proteins.

Protein-Ligand Benchmark Dataset for Free Energy Calculations

Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023

InteractionGraphNet: a Novel and Efficient Deep Graph Representation Learning Framework for Accurate Protein-Ligand Interaction Prediction and Large-scale Structure-based Virtual Screening

A nano protein structure prediction model based on DeepMind's AlphaFold paper

Implementation of Alphafold 3 in Pytorch

Fast and accurate protein domain segmentation using Invariant Point Attention

Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch

3D equivariant graph transformer for all-atom refinement of protein tertiary structures

Pretrain, finetune ANY AI model of ANY size on multiple GPUs, TPUs with zero code changes.

A collection of resources and papers on Diffusion Models

NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

python tools for TCR:peptide-MHC modeling and analysis

[AAAI'24] DiSCO: Diffusion Schrödinger Bridge for Molecular Conformer Optimization

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

DeeplyTough: Learning Structural Comparison of Protein Binding Sites