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pros-gnn

protease-gcnn-pytorch

protein-interaction-network

Computes a molecular graph for protein structures.

protein-ligand-interaction-graphs

protein-sequence-embedding-iclr2019

Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019

proteinfer

proteingan

proteingraph

proteingraphml

Protein Graph in Python for MetaPath-ML and more.

protgraph

ProtGraph - A Graph-Generator for Proteins

prottrans

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

pv

WebGL protein viewer

pybiomed

machine learning, molecular descriptor

pychimera

Use UCSF Chimera Python API in a standard interpreter

pyenzyme

🧬 - Data management and modeling framework based on EnzymeML.

pyfaidx

Efficient pythonic random access to fasta subsequences

pyrosetta.notebooks

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

pytorch_active_learning

PyTorch Library for Active Learning to accompany Human-in-the-Loop Machine Learning book

pytorch_geometric

Graph Neural Network Library for PyTorch

qmmm-workshop

Workshop teaching QMMM using Amber

quick

QUICK: A GPU-enabled ab intio quantum chemistry software package

rankfm

Factorization Machines for Recommendation and Ranking Problems with Implicit Feedback Data

rd_filters

A script to run structural alerts using the RDKit and ChEMBL

rdchiral

Wrapper for RDKit's RunReactants to improve stereochemistry handling

rdkit

The official sources for the RDKit library

rdkit-blog

rdkit-cats2d

Modification of the code of Rajarshi Guha (which uses OECHem) to use RDKIT.

retropathrl

Reinforcement Learning based bioretrosynthesis tool

rf-score

A machine learning approach to predicting protein-ligand binding affinity.

rita

RITA is a family of autoregressive protein models, developed by LightOn in collaboration with the OATML group at Oxford and the Debora Marks Lab at Harvard.