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af_cluster

Predict multiple protein conformations using sequence clustering and AlphaFold2.

alphafold

Open source code for AlphaFold.

antiberty

Antibody-specific masked language model

chroma

A generative model for programmable protein design

dssp

Application to assign secondary structure to proteins

dynamicbind

repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model

egnn

esm

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

fairseq

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

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

geom

GEOM: Energy-annotated molecular conformations

gvp

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

igfold

Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies

libauc

An end-to-end machine learning library to directly optimize AUC (AUROC, AUPRC)

lifanchen-simm.github.io

lookahead.pytorch

lookahead optimizer (Lookahead Optimizer: k steps forward, 1 step back) for pytorch

machine-learning-for-proteins

Listing of papers about machine learning for proteins.

masif_seed

Masif seed paper repository

multidim-positional-encoding

An implementation of 1D, 2D, and 3D positional encoding in Pytorch and TensorFlow

neuralplexer

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

openfold

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

performer-pytorch

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

phate

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.

picture-1

posebusters

Plausibility checks for generated molecule poses.

pytorch_geometric

Geometric Deep Learning Extension Library for PyTorch

r-drop

radam

On The Variance Of The Adaptive Learning Rate And Beyond

rosettafold-all-atom

saprot