An automated and interoperable manager for computational chemistry workflows.

toolkit for prediction pKa values of small molecules via graph convolutional networks

Machine Learning model for molecular micro-pKa prediction

A user-friendly application for precise conformation sampling

Generates and scores synthetically tractable elaborations from fragment screens

an integrated tool for molecular docking and virtual screening

OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method

In silico directed evolution of peptide binders with AlphaFold

Free Parametrization for Small Molecules

A hyperparameter optimization framework

Code to perform scaffold hopping and virtual screening using WHALES descriptors.

python code for calculating the WHALES (Weighted Holistic Atom Localization and Entity Shape) molecular descriptors

As part of the solubility app development, this notebook was used to select and train machine learning model

Datagrok repository for ADMET property evaluation

A snakemake-based workflow for FEP and MM(PB/GB)SA calculations with GROMACS

An interoperable Python framework for biomolecular simulation.

Revised breaking of retrosynthetically interesting chemical substructures (r-BRICS) – a revised BRICS module based on rdKit that breaks ring structures and carbon chains

OpenMM tutorial for the MSBS course

Automatic gromacs protocol from preparation to production with ligand parametrization through

A collection of cheminformatics scripts that use rdkit

Generate molecular fingerprints using RDKit

BindCraft modified to make PyRosetta use and installation optional: no license needed

Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertubation with OpenMM.