anton-bushuiev

PPIRef

Dataset and package for working with protein-protein interactions in 3D

PPIformer

Learning to design protein-protein interactions with enhanced generalization (ICLR24)

mutils

Mutation utilities for protein design

MassSpecGym

MassSpecGym: A benchmark for the discovery and identification of molecules

SE3Transformer

Copy from https://github.com/NVIDIA/DeepLearningExamples

anton-bushuiev

arctic3d

Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information

biopandas

Working with molecular structures in pandas DataFrames

DiGress

code for the paper "DiGress: Discrete Denoising diffusion for graph generation"

distributed-max-bipartite-subgraph

equiformer-pytorch

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

esm

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

GeoPPI-plus-plus

graphein

Protein Graph Library

MuPIPR

pytorch

Tensors and Dynamic neural networks in Python with strong GPU acceleration

pytorch_geometric

Graph Neural Network Library for PyTorch

RDE-PPI

:mountain: Rotamer Density Estimator is an Unsupervised Learner of the Effect of Mutations on Protein-Protein Interaction (ICLR 2023)

DreaMS

DreaMS (Deep Representations Empowering the Annotation of Mass Spectra)

flex_ddG_tutorial

mist

Encoding MS/MS spectra using formula transformers for inferring molecular properties

mutils-ICLR2024-rebuttal-

PPIformer-ICLR2024-rebuttal

PPIRef-ICLR2024-rebuttal

Scientific-Programming-in-Julia

Repository for B0M36SPJ

scikit-learn

scikit-learn: machine learning in Python

SuperGluePretrainedNetwork

SuperGlue: Learning Feature Matching with Graph Neural Networks (CVPR 2020, Oral)