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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87 of 7,083 resources
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Parameter/topology editor and molecular simulator with visualization capability.
Provides functionality for producing geometric representations of protein and RNA structures, and biological interaction networks.
Ensemble of automated machine learning protocols that can be run sequentially through a single command line. The program works for regression and classification problems.
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.
A collection of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and transport processes.
A benchmark for ML-guided high-throughput materials discovery.
Python Library for Automating Molecular Simulation: input preparation, job execution, file management, output processing and building data workflows.
PyTorch toolkit for deep neural networks in atomistic simulations, implementing SchNet, DimeNet++, PaiNN, and GemNet for molecular dynamics and quantum chemistry (900+ stars)
High-Throughput Molecular Dynamics: Programming Environment for Molecular Discovery.
A toolkit for visualizations in materials informatics.
Ensemble of automated QM workflows that can be run through jupyter notebooks, command lines and yaml files.
Quantum chemisttry web platform that brings all the necessary tools to perform quantum chemistry in a user-friendly web interface.
Convert AMBER forcefields from ANTECHAMBER to GROMACS format.
A library for processing, analyzing and modeling spectroscopic data.
Universal pretrained neural network potential with charge and magnetic moment awareness, trained on 1.5M+ Materials Project inorganic structures for charge-informed molecular dynamics and phase diagram prediction (Berkeley, Nature Machine Intelligence 2023 Cover)
Open source PEM (Proton Exchange Membrane) fuel cell simulation tool.
The "FRamewOrk for Molecular AGgregate Excitations" enables localised QM/QM' excited state calculations in a solid state environment.
The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools.
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
- Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.
Library of descriptors to aid in the data-mining of materials properties, created by the Lawrence Berkeley National Laboratory.
Scientific Computing for Chemists with Python is a Jupyter book teaching basic python in chemistry skills, including relevant libraries, and applies them to solving chemical problems.
A Simulation Tool for Fractured and Deformable Porous Media.
High-throughput PubChem client for batch queries with caching, validation, rate-limit-aware retries, and a simple CLI.
A package to 'build' collections of materials properties from the output of computational materials calculations.
Library for fast calculations of **mo**lecula**r** **fe**at**u**re**s** from 3D structures for machine learning with a focus on steric descriptors.
Directed message passing neural networks for property prediction of molecules and reactions with uncertainty and interpretation.
An interactive structure/property explorer for materials and molecules.
A molecule manipulation library.
atomate2 is a library of computational materials science workflows.
A library containing basis sets for use in quantum chemistry calculations. In addition, this library has functionality for manipulation of basis set data.
A library and command-line tool for building and analyzing complex homogeneous microkinetic models from quantum chemistry calculations, with support for quasi-harmonic thermochemistry, quantum tunnelling corrections, molecular symmetries and more.
A package for working with nuclear magnetic resonance (NMR) data including functions for reading common binary file formats and processing NMR data.
A quantum chemistry package written in Python.
Calculate mass, elemental composition, and mass distribution spectrum of a molecule given by its chemical formula, relative element weights, or sequence.
Interaction Fingerprints for protein-ligand complexes and more.
Predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
Aims to provide useful high-level interfaces that make ML for materials science as easy as possible.
Neural Network Force Field based on PyTorch.
A package for creating fast and accurate interatomic potentials.
A tool and library for creating quantum chemistry input files.
This package provides a periodic table of the elements with support for mass, density and xray/neutron scattering information.
Makes alchemical free energy calculations easier by leveraging the full power and flexibility of the PyData stack.
Automate downloading, opening, and parsing DrugBank.
A package for accessing data from the NIST webbook...
Simple RDKit molecule editor GUI using PySide.
End-to-end molecular dynamics engine built on PyTorch, enabling differentiable simulations with neural network potentials and GPU acceleration for machine learning-accelerated molecular dynamics (MIT License, 707+ stars)
Descriptor library containing a variety of fingerprinting techniques, including the Smooth Overlap of Atomic Positions (SOAP).
AstraZeneca's industrial-grade retrosynthetic planning tool using MCTS to recursively decompose molecules into purchasable precursors, with multi-step route scoring and support for custom one-step models (v4.0, 2024)