heiidii Goto Github PK

messagepassinggnns

DGL implementation of Gtransformer layers

neurips19-graph-protein-design

Generative Models for Graph-Based Protein Design

pglb_scripts

ppiformer

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

progen

Official release of the ProGen models

proteinmpnn

Code for the ProteinMPNN paper

proteinworkshop

Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities.

provis

Official code repository of "BERTology Meets Biology: Interpreting Attention in Protein Language Models."

pytorch-grad-cam

Many Class Activation Map methods implemented in Pytorch for CNNs and Vision Transformers. Including Grad-CAM, Grad-CAM++, Score-CAM, Ablation-CAM and XGrad-CAM

rosetta

The Rosetta Bio-macromolecule modeling package.

scripts

Scripts used for analyzing data generated from simulations

se3-transformer-public

code for the SE3 Transformers paper: https://arxiv.org/abs/2006.10503

segment-anything

The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.

sidechainnet

An all-atom protein structure dataset for machine learning.

tape

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

trrosetta

A package to predict protein inter-residue geometries from sequence data

unirep

UniRep model, usage, and examples.