Find open-source science resources
A directory of tools, AI models, datasets, and research resources for biotech, bioinformatics, and other scientific fields. Aggregated from curated GitHub awesome-lists, HuggingFace, bio.tools, Bioconductor, and more.
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45 of 5,893 resources
A teaching platform for computer-aided drug design (CADD) using open source packages and data.
An object-oriented, webGL based JavaScript library for online molecular visualization.
A swiss army knife for manipulating and editing PDB files.
A Python package useful for chemistry (mainly physical/inorganic/analytical chemistry)
Directed message passing neural networks for property prediction of molecules and reactions with uncertainty and interpretation.
A Python package for protein dynamics analysis
Deep learning library for Chemistry based on Tensorflow
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.
[RDKit](http://www.rdkit.org/) and [OSRA](https://cactus.nci.nih.gov/osra/) in the [Bottle](http://bottlepy.org/docs/dev/) on [Tornado](http://www.tornadoweb.org/en/stable/).
OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend.
DGL-LifeSci is a [DGL](https://www.dgl.ai/)-based package for various applications in life science with graph neural network.
A curated list of molecular docking software, datasets, and other closely related resources.
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.
Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows
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.
A graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia
- Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.
Molecule validation and standardization based on [RDKit](http://www.rdkit.org/).
A script to run structural alerts using the RDKit and ChEMBL
Chemical 2D structure editor application/applet based on the [Chemistry Development Kit](https://sourceforge.net/projects/cdk/).
Simple RDKit molecule editor GUI using PySide.
Molecular descriptor calculator based on [RDKit](http://www.rdkit.org/).
Descriptor computation(chemistry) and (optional) storage for machine learning.
Vector representations of molecular substructures.
ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data. (based on Tensorflow)
Molecular property prediction with unified API for diverse models and respresentations,
A Library for Deep Learning in Biology and Chemistry.
A python package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks).
Open source web framework for small molecule analysis based on Django.
Automates and standardizes ligand preparation for AutoDock Vina.
Analysis of molecular dynamics trajectories.
Parsers and algorithms for computational chemistry logfiles.
The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.
an automated workflow for the generation and storage of DFT calculations for organic molecules.
Chemoinformatics and drug discovery section in deeplearning-biology repo.
A list of papers, data sets, and other resources for machine learning for small-molecule drug discovery.