lmqfly

MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

HowToTrainYourMAMLPytorch

The original code for the paper "How to train your MAML" along with a replication of the original "Model Agnostic Meta Learning" (MAML) paper in Pytorch.

GET

This repo contains the codes for our paper "Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning" (ICML 2024).

DEM

Code for the paper Iterated Denoising Energy Matching for Sampling from Boltzmann Densities.

EigenFold

EigenFold: Generative Protein Structure Prediction with Diffusion Models

SurfDock

SurfDock is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein-ligand Complex Prediction

EquiScore

awesome-BioMolFold

RNA, mRNA, DNA, Peptide, Protein, Antibody and Complex | Folding

awesome-AI4MolConformation-MD

List of molecules (small molecules, RNA, peptide, protein, enzymes, antibody, and PPIs) conformations and molecular dynamics (force fields) using generative artificial intelligence and deep learning

masif

MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.

AlphaPPImd

Exploring the conformational ensembles of protein-protein complexes with transformer-based generative neural networks

neurips19-graph-protein-design

Generative Models for Graph-Based Protein Design

gvp-pytorch

Geometric Vector Perceptrons --- a rotation-equivariant GNN for learning from biomolecular structure

ProteinMPNN

Code for the ProteinMPNN paper

geometric-gnn-dojo

Geometric GNN Dojo provides unified implementations and experiments to explore the design space of Geometric Graph Neural Networks.

Geometry-Deep-Learning-for-Drug-Discovery

Geometry Deep Learning for Drug Discovery and Life Science

ProtMD

CGIP

A simple and effective Contrastive Graph-Image Pre-training framework for molecular representation learning (BIB 2023)

DiffDock

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

MDAnalysisData

Access to data for workshops and extended tests of MDAnalysis.

transformer

Transformer: PyTorch Implementation of "Attention Is All You Need"

molarxiv

misato-dataset

equiformer-pytorch

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

GIGN

MiSaTo-dataset

ogb

Benchmark datasets, data loaders, and evaluators for graph machine learning

equiformer

[ICLR'23 Spotlight] Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs

p2rank

P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.

TankBind

Open source code for TankBind. Galixir Tenchnologies