Find open-source science resources

Provides functionality for producing geometric representations of protein and RNA structures, and biological interaction networks.

Quantum chemisttry web platform that brings all the necessary tools to perform quantum chemistry in a user-friendly web interface.

A library for building, manipulating, analyzing and automatic design of molecules, including a genetic algorithm.

A Package For Training SNAP Interatomic Potentials for use in the LAMMPS molecular dynamics package.

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).

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)

Experiments with expanded ensembles to explore chemical space.

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 Jupyter book demonstrating working with biochemical data using the scikit-bio library for tasks such as sequence alignment and calculating Hamming distances.

Automate downloading, opening, and parsing DrugBank.

Automate downloading and querying the latest (or a given) version of ChEMBL.

A package for accessing data from the NIST webbook...

High-throughput PubChem client for batch queries with caching, validation, rate-limit-aware retries, and a simple CLI.

Jupyter Widgets to interact with molecular datasets.

A [Jupyter](https://jupyter.org/) widget to interactively view molecular structures and trajectories.

A molecule manipulation library.

An interactive structure/property explorer for materials and molecules.

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools.

Neural Network Force Field based on PyTorch.

A benchmark for ML-guided high-throughput materials discovery.

A Chemical Knowledge Graph and Toolkit, writting in IUPAC/SMILES/SMARTS, for common small molecules from diverse communities to aid users in selecting compounds for forcefield parametirization.

A package for creating fast and accurate interatomic potentials.

Tool to build force field input files for molecular simulation.

Convert AMBER forcefields from ANTECHAMBER to GROMACS format.

An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.

A module for solving and visualizing the Schrödinger equation.

Usage-Instructions) - A program to visualize reaction networks.

A quantum chemistry package written in Python.

A calculator incorporating various empirical pair and many-body potentials.

Psi4-based reference implementations and Jupyter notebook-based tutorials for foundational quantum chemistry methods.

Interaction Fingerprints for protein-ligand complexes and more.

A Simulation Tool for Fractured and Deformable Porous Media.

Python Library for Automating Molecular Simulation: input preparation, job execution, file management, output processing and building data workflows.

A library for estimating thermochemical properties of molecules and adsorbates using group additivity.

Parameter/topology editor and molecular simulator with visualization capability.

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 batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

Open source PEM (Proton Exchange Membrane) fuel cell simulation tool.

Open Drug Discovery Toolkit, a modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc.

File parser/converter for QM, MD and plane-wave DFT programs.

High-Throughput Molecular Dynamics: Programming Environment for Molecular Discovery.

The "FRamewOrk for Molecular AGgregate Excitations" enables localised QM/QM' excited state calculations in a solid state environment.

A package to 'build' collections of materials properties from the output of computational materials calculations.

A library for computational chemistry (DFT) for input file generation, data extraction, method screening and analysis.

A tool and library for creating quantum chemistry input files.

General purpose tools for high-throughput catalysis.

A collection of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and transport processes.

A library containing basis sets for use in quantum chemistry calculations. In addition, this library has functionality for manipulation of basis set data.

atomate2 is a library of computational materials science workflows.

Makes alchemical free energy calculations easier by leveraging the full power and flexibility of the PyData stack.