Find open-source science resources

A Python package for protein dynamics analysis

Universal molecular toolkit that can be used for molecular fingerprinting, substructure search, and molecular visualization written in C++ package, with Java, C#, and Python wrappers.

Descriptor computation(chemistry) and (optional) storage for machine learning.

Chemical 2D structure editor application/applet based on the [Chemistry Development Kit](https://sourceforge.net/projects/cdk/).

Analysis of molecular dynamics trajectories.

Parsers and algorithms for computational chemistry logfiles.

An object-oriented, webGL based JavaScript library for online molecular visualization.

ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data. (based on Tensorflow)

- Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.

Directed message passing neural networks for property prediction of molecules and reactions with uncertainty and interpretation.

Chemical Information from the Web.

A teaching platform for computer-aided drug design (CADD) using open source packages and data.

Deep learning library for Chemistry based on Tensorflow

Open Parser for Systematic IUPAC nomenclature

A Python package useful for chemistry (mainly physical/inorganic/analytical chemistry)

Chemoinformatics and drug discovery section in deeplearning-biology repo.

A swiss army knife for manipulating and editing PDB files.

A graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia

Automates and standardizes ligand preparation for AutoDock Vina.

Simple RDKit molecule editor GUI using PySide.

A script to run structural alerts using the RDKit and ChEMBL

an automated workflow for the generation and storage of DFT calculations for organic molecules.

Webapp for generating conformers

Python-centric Cookiecutter for Molecular Computational Chemistry Packages by [MolSSL](https://molssi.org/)

Tool designed to provide a simple way of standardising molecules as a prelude to e.g. molecular modelling exercises.

A Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models in R.

Another list focuses on Python stuff related to Chemistry.

Cheminformatic extension for the SQLAlchemy database.

The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.

A python package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks).

Molecular descriptor calculator based on [RDKit](http://www.rdkit.org/).

OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend.

A list of papers, data sets, and other resources for machine learning for small-molecule drug discovery.

DGL-LifeSci is a [DGL](https://www.dgl.ai/)-based package for various applications in life science with graph neural network.

Wrapper for RDKit's RunReactants to improve stereochemistry handling

A Library for Deep Learning in Biology and Chemistry.

A curated list of molecular docking software, datasets, and other closely related resources.

Open source web framework for small molecule analysis based on Django.

Toolkit for processing molecules, reactions and condensed graphs of reactions. Can be used for chemical standardization, MCS search, tautomers generation with backward compatibility to RDKit and NetworkX.

Molecule validation and standardization based on [RDKit](http://www.rdkit.org/).

Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows

Molecular property prediction with unified API for diverse models and respresentations,