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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

esm3

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

hlafreq

Aggregate HLA allele frequencies data from allelefrequencies.net at large multi population scale

igfold

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

kinomemeta

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

offtarget_drugsafety

In Silico Off-Target Profiling for Enhanced Drug Safety Assessment

olga

Compute generation probabilities of CDR3 amino acid and nucleotide sequences

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.