masif

MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

microfrontend-resources

:fire: A curated list of resources about Micro frontends grouped by types

neurips19-graph-protein-design

Generative Models for Graph-Based Protein Design

neuroseed

Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)

ngl

WebGL protein viewer

nglview

IPython widget to interactively view molecular structures and trajectories

oceanic-reef-terminal

Oceanic Reef theme for Terminal (Mac OS X)

openfold

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

paragraph

Antibody paratope prediction using Graph Neural Networks with minimal feature vectors

parapred

Paratope Prediction using Deep Learning

pdb-wise-analysis

PDB wise analysis topcis

pdbe-molstar

Molstar PDBe implementation

pecan

Help file for running the scripts to learn and evaluate graph convolution networks for epitope and paratope prediction

practical-c-programming

Practical C Programming, published by Packt

pre-training-via-denoising

Official implementation of pre-training via denoising for TorchMD-NET

pretrain-gnns

Strategies for Pre-training Graph Neural Networks

probability

Probabilistic reasoning and statistical analysis in TensorFlow

proteinfeatureview

:round_pushpin: The Protein Feature View - a SVG library for visualising protein annotations

proteinnet

Standardized data set for machine learning of protein structure

pymol-script-repo

Collected scripts for Pymol

pyrosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

pytorch-vae

A Collection of Variational Autoencoders (VAE) in PyTorch.

pytorchgeometrictutorial

Pytorch Geometric Tutorials

repo-badges

:star: Use repo badges (build passing, coverage, etc) in your readme/markdown file to signal code quality in a project.

rfdesign

Protein hallucination and inpainting with RoseTTAFold

rgn

Recurrent Geometric Networks for end-to-end differentiable learning of protein structure

saap3

The SAAPdap/SAAPpred software and web interface

sagemaker-documentdb-train-gnn-for-millions-proteins

Training graph neural nets for millions of proteins on Amazon SageMaker and DocumentDB.

scannet