Installable VMD as a python module

Simple package for fast molecular similarity searches

Code for paper "Human-in-the-Loop Assisted de Novo Molecular Design".

Code for paper "Human-in-the-Loop Assisted de Novo Molecular Design".

Evaluation of Reinforcement Learning in Transformer-based Molecular Design

Utilities for working with SMILES based encodings of molecules for deep learning (PyTorch oriented)

Tools to train synthesis prediction models

QSARtuna: QSAR model building with the optuna framework

UQ4DD: Uncertainty Quantification for Drug Discovery

Utilities for working with datasets of chemical reactions, reaction templates and template extraction.

Tools and routines to calculate distances between synthesis routes and to cluster them.

Repository for training, evaluating and using synthesis prediction models

AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.

Automate seekr handling with seekrflow to decrease time and manual intervention to complete seekr calculations.

An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculation.

Uni-Dock-Benchmarks contains a curated collection of datasets and benchmarking tests for evaluating the performance and accuracy of the Uni-Dock docking system. This repository is intended for use …

Uni-FEP-Benchmarks is a benchmark dataset designed to systematically evaluate Uni-FEP.

TOFF (Topologies from OpenFF) is a python package to get topologies from the OpenFF initiative for MD simulations

Streamlit component that use JSME to draw 2D molecules and use them on your Streamlit app

moldrug (AKA mouse) is a Python package for drug-oriented optimization on the chemical space ​

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

Everything to reproduce BindFlow results

Benchmarks for generative chemistry

an efficient distributed PyTorch framework