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alphafold

Open source code for AlphaFold.

geometric-gnn-dojo

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

PiFold

The official implementation of the ICLR'23 paper PiFold: Toward effective and efficient protein inverse folding.

RFdiffusion

Code for running RFdiffusion

afnmr

Tools to compute NMR chemical shifts for biomolecules

gvp-pytorch

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

SubGNN

Subgraph Neural Networks (NeurIPS 2020)

DiffDock

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

OmegaFold

OmegaFold Release Code

ScanNet

practical_cheminformatics_tutorials

Practical Cheminformatics Tutorials

equidock_public

EquiDock: geometric deep learning for fast rigid 3D protein-protein docking

bgflow

Boltzmann Generators and Normalizing Flows in PyTorch

mldl-md-dynamics

A repository of update in molecular dynamics field by recent progress in machine learning and deep learning.

paper_boltzmann_generators

teachopencadd

TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

openmm-torch

OpenMM plugin to define forces with neural networks

ProtTrans

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

tape

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

PaddleHelix

Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集

performer-pytorch

An implementation of Performer, a linear attention-based transformer, in Pytorch

Machine-learning-for-proteins

Listing of papers about machine learning for proteins.

sidechainnet

An all-atom protein structure dataset for machine learning.

pybind11

Seamless operability between C++11 and Python

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

proteinnet

Standardized data set for machine learning of protein structure

Long-Tailed-Recognition.pytorch

[NeurIPS 2020] This project provides a strong single-stage baseline for Long-Tailed Classification, Detection, and Instance Segmentation (LVIS). It is also a PyTorch implementation of the NeurIPS 2020 paper 'Long-Tailed Classification by Keeping the Good and Removing the Bad Momentum Causal Effect'.

Adabelief-Optimizer

Repository for NeurIPS 2020 Spotlight "AdaBelief Optimizer: Adapting stepsizes by the belief in observed gradients"

OpenNMT-tf

Neural machine translation and sequence learning using TensorFlow