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 5,923 resources
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The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools.
An interactive structure/property explorer for materials and molecules.
A Simulation Tool for Fractured and Deformable Porous Media.
This package provides a periodic table of the elements with support for mass, density and xray/neutron scattering information.
A molecule manipulation library.
atomate2 is a library of computational materials science workflows.
A quantum chemistry package written in Python.
Provides functionality for producing geometric representations of protein and RNA structures, and biological interaction networks.
Automate downloading, opening, and parsing DrugBank.
A package for accessing data from the NIST webbook...
Interaction Fingerprints for protein-ligand complexes and more.
A collection of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and transport processes.
Directed message passing neural networks for property prediction of molecules and reactions with uncertainty and interpretation.
Descriptor library containing a variety of fingerprinting techniques, including the Smooth Overlap of Atomic Positions (SOAP).
Parameter/topology editor and molecular simulator with visualization capability.
Tool to build force field input files for molecular simulation.
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.
Predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
Quantum chemisttry web platform that brings all the necessary tools to perform quantum chemistry in a user-friendly web interface.
A library containing basis sets for use in quantum chemistry calculations. In addition, this library has functionality for manipulation of basis set 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)
Neural Network Force Field based on PyTorch.
A package for working with nuclear magnetic resonance (NMR) data including functions for reading common binary file formats and processing NMR data.
File parser/converter for QM, MD and plane-wave DFT programs.
A package for creating fast and accurate interatomic potentials.
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.
Automate downloading and querying the latest (or a given) version of ChEMBL.
Therapeutics Data Commons: 66 AI-ready datasets across 22 drug discovery tasks with 29 leaderboards, covering target identification, molecular generation, ADMET prediction, and clinical trial outcomes (Harvard MIMS, NeurIPS 2021/2024)
A library for estimating thermochemical properties of molecules and adsorbates using group additivity.
General purpose tools for high-throughput catalysis.
A module for solving and visualizing the Schrödinger equation.
A Deep Learning Library for Compound and Protein Modeling DTI, Drug Property, PPI, DDI, Protein Function Prediction.
A package for benchmarking of models for _de novo_ molecular design.
Psi4-based reference implementations and Jupyter notebook-based tutorials for foundational quantum chemistry methods.
A Jupyter book demonstrating working with biochemical data using the scikit-bio library for tasks such as sequence alignment and calculating Hamming distances.
Graph Networks as a Universal Machine Learning Framework for Molecules and Crystals.
A deep learning framework (based on Chainer) with applications in Biology and Chemistry.
A platform for graph-based molecular generation using graph neural networks.
Enables machine learning on three-dimensional molecular structure.
a robust molecular representation learning framework against distribution shifts.
Open Drug Discovery Toolkit, a modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc.
Hierarchical Generation of Molecular Graphs using Structural Motifs.
Jupyter Widgets to interact with molecular datasets.
A calculator incorporating various empirical pair and many-body potentials.
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.
- Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.