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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62 of 7,083 resources
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Parameter/topology editor and molecular simulator with visualization capability.
Ensemble of automated machine learning protocols that can be run sequentially through a single command line. The program works for regression and classification problems.
Descriptor computation(chemistry) and (optional) storage for machine learning.
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)
A toolkit for visualizations in materials informatics.
Ensemble of automated QM workflows that can be run through jupyter notebooks, command lines and yaml files.
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.
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.
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.
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)
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)
Tool to build force field input files for molecular simulation.
File parser/converter for QM, MD and plane-wave DFT programs.
A library for building, manipulating, analyzing and automatic design of molecules, including a genetic algorithm.
ChemFormula provides a class for working with chemical formulas. It allows parsing chemical formulas, calculating formula weights, and generating formatted output strings (e.g. in HTML, LaTeX, or Unicode).
A library for computational chemistry (DFT) for input file generation, data extraction, method screening and analysis.
Experiments with expanded ensembles to explore chemical space.
A Package For Training SNAP Interatomic Potentials for use in the LAMMPS molecular dynamics package.
NIST's open-source platform for data-driven atomistic materials design, integrating DFT datasets (JARVIS-DFT), machine learning property prediction (JARVIS-ML), and a comprehensive leaderboard for benchmarking materials AI methods across the periodic table (384+ stars)
A library for estimating thermochemical properties of molecules and adsorbates using group additivity.
General purpose tools for high-throughput catalysis.
Self-Referencing Embedded Strings (SELFIES): A 100% robust molecular string representation.