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pythonalgo

All Algorithms implemented in Python

qube-somd-paper

ramachandraw

Ramachandran plotting tool.

rascore

Retrosynthetic Accessibility (RA) score learned from computer aided synthesis planning

rdchiral

Wrapper for RDKit's RunReactants to improve stereochemistry handling

rdkit

The official sources for the RDKit library

rdkit-blog

rdkit-scripts

A collection of cheminformatics scripts that use rdkit

reeds

This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.

reinvent-randomized

Recurrent Neural Network using randomized SMILES strings to generate molecules

reinvent-scaffold-decorator

A SMILES-based encoder-decoder architecture for molecular scaffold decoration

reinventcommunity

release

Deep Reinforcement Learning for de-novo Drug Design

sampl6

Challenge inputs, details, and results for the SAMPL6 series of challenges

scaffoldgraph

ScaffoldGraph is an open-source cheminformatics library, built using RDKit and NetworkX, for the generation and analysis of scaffold networks and scaffold trees.

scikit-learn

scikit-learn: machine learning in Python

sire

Sire Molecular Simulations Framework

siremol.org

Code for my websites

stoned-selfies

This repository contains code for the paper: Beyond Generative Models: Superfast Traversal, Optimization, Novelty, Exploration and Discovery (STONED) Algorithm for Molecules using SELFIES

strife

syba

Synthetic Bayesian Classification

tautobase

Contains relevant project files to publicly available tautomer database "Tautobase" for DataWarrior

ties_md

Python package built on OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.

torchdrug

A powerful and flexible machine learning platform for drug discovery

ttclust

clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)

virtual_libraries

Supporting code for the paper «Generative molecular design in low data regimes»

xyz2mol

Converts an xyz file to an RDKit mol object