Facebook AI Research Sequence-to-Sequence Toolkit written in Python.

Open source code for AlphaFold.

Denoising Diffusion Probabilistic Models

This may be the simplest implement of DDPM. You can directly run Main.py to train the UNet on CIFAR-10 dataset and see the amazing process of denoising.

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

Implementation of Alphafold 3 in Pytorch

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

Implementation of MolCLR: "Molecular Contrastive Learning of Representations via Graph Neural Networks" in PyG.

Computational Crystallography Toolbox

DockQ is a single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models

Geometric Latent Diffusion Models for 3D Molecule Generation

This is a code for compound-protein interaction (CPI) prediction based on a graph neural network (GNN) for compounds and a convolutional neural network (CNN) for proteins.

A Python package for processing molecules with RDKit in scikit-learn

Official repo of the modular BioExcel version of HADDOCK

Python interface for the RCSB PDB search API.

Official implementation of Generative Diffusion Models for Antibody Design, Docking, and Optimization.

pre-training BERT with molecular data

AlphaFold-initiated replica exchange protein docking

HIPPOS Is PyPLIF On Steroids. A Molecular Interaction Fingerprinting Tool for Docking Results of Autodock Vina and PLANTS

SPVec: A Word2vec-inspired feature representation method for Drug-Target Interaction Prediction

Fast AlphaFold-Multimer based pipeline for Protein-Protein Interaction (PPI) screening

[NeurIPS 2024] MSA generative pretraining for advancing protein structure prediction

scripts for parsing PDB, fasta, and GO

This repository is the official implementation of "Hyperbolic Geometric Latent Diffusion Model for Graph Generation (HypDiff)" accepted by the research tracks of International Conference on Machine…

[Bioinformatics 2022] Cross-Modality and Self-Supervised Protein Embedding for Compound-Protein Affinity and Contact Prediction