OMSF Directory

A high-throughput alchemical free energy execution system for OpenFE Protocols. Built for use with HPC, cloud, bare metal, and Folding@Home.

A framework for molecular modeling and mechanics written in Julia

BiochemicalVisualization.jl is the graphical interface for BiochemicalAlgorithms.jl, providing different representations for biomolecular systems. All representations can be visualized in the form of interactive web widgets that are embeddable in Jupyter notebooks.

A deep learning model that samples from the approximated equilibrium distribution of structures for a protein monomer, given its amino acid sequence. It can generate thousands of statistically independent structures from the protein structure ensemble per hour on a single GPU.

Biotite is your Swiss army knife for bioinformatics. Whether you want to identify homologous sequence regions in a protein family or you would like to find disulfide bonds in a protein structure: Biotite has the right tool for you. This package bundles popular tasks in computational molecular biology into a uniform Python library.

Cinnabar is a software package designed to reliably report and visualize relative free energy results from molecular simulations.

Egret is a family of open-source neural network potentials for bioorganic simulation.

eOn provides a C++ client for atomistic calculations, including saddle search methods with machine learned potentials and a Python server for long time scale dynamics.

Exorcist is a daemonless campaign-scale simulation orchestration tool designed to streamline the management of simulation tasks.

Feflow provides community-generated OpenMM-based Protocols for OpenFE. Currently implements a non-equilibrium cycling hybrid topology Protocol based on Perses.

Systematic force field optimization

An open-source Python tool that provides a framework for the application and dissemination of classical molecular modeling force fields.

GMSO is a flexible storage of chemical topology for various molecular simulation engines.

A free and open-source software suite for high-performance molecular dynamics simulations and trajectory analysis.

GUFE is a toolkit for developers of software related to alchemical free energy calculations, containing data models and abstract base classes.

Gives information about possible isotopes of a molecule: isotopic content, mass, abundance, relative intensity of a signal in a Mass Spectrometer. You can get all isotopologues of a molecule sorted from the most common to the rarest.

Kartograf is a package for creating atom mappings for alchemical simulations using a 3D geometric graph-based algorithm.

A fast, multi-threaded PDB parser library written in Rust with Python bindings.

Konnektor is a package supporting efficient planning of free energy calculations through advanced network algorithms and tools.

Large-scale Atomic/Molecular Massively Parallel Simulator for molecular dynamics and particle simulations.

A hierarchical, component based molecule builder for initializing atomistic and coarse-grained coordinates and connectivity.

MDAnalysis is a Python library to analyze molecular dynamics simulations.

An open library for the analysis of molecular dynamics trajectories

Molecular simulation in Julia

High-performance parallel molecular dynamics program for large-scale biomolecular systems

IPython/Jupyter widget to interactively view molecular structures and trajectories

The main software package for the OpenADMET Project. openadmet-models implements machine learning workflows for predicting ADMET properties of small molecules including our ANVIL training and evaluation workflows

The main software package for the Open Free Energy Project. openfe implements a series of alchemical free energy Protocols and tooling to use them, including a CLI interface.

The BespokeFit framework aims to offer a completely automated workflow for creating bespoke, highly accurate, SMIRNOFF format parameters for individual molecules up to entire lead series.

The OpenFF Evaluator is a scalable framework for the automated estimation of physical property data sets from molecular simulation and molecular simulation data.

This repository contains force fields released by the Open Force Field Initiative using the SMIRKS Native Open Force Field (SMIRNOFF) format.

A package for fragmenting molecules for quantum mechanics torsion scans.

A project for storing, manipulating, and converting molecular mechanics data and supports parametrization and export to common formats.

A playground for applying graph convolutional networks to molecules, with a focus on learning continuous "atom-type" embeddings and from these classical molecule force field parameters.

This repository contains NAGL models released by the Open Force Field Initiative, intended for use with OpenFF NAGL.

The OpenFF QCSubmit framework aims to facilitate curating and contributing new quantum chemical datasets to the QCArchive and retrieving already computed datasets.

OpenFF Recharge aims to provide a comprehensive suite of tools for training the partial charges of molecules against quantum chemical electrostatic potential (ESP) and electric field data.

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

A common units module for the OpenFF software stack, providing consistent unit definitions across the software ecosystem.

A collection of miscellaneous utility functions used throughout the OpenFF stack.

A trainable PyTorch reproduction of DeepMind's AlphaFold2.

A fully open source biomolecular structure prediction model based on AlphaFold3

High-performance toolkit for molecular simulation

A package for building initial configurations for molecular dynamics simulations by packing molecules in defined regions of space with spatial constraints.

Deep learning based protein sequence design method is described that is widely applicable to current design challenges and shows outstanding performance in both in silico and experimental tests.

An open-source ab initio quantum chemistry software package

PyMPFIT provides a comprehensive suite of tools for training the partial charges of molecules against quantum chemical Gaussian distributed multipole analysis (GDMA) data. Features include multi-molecule constrained optimization and Bayesian virtual site fitting.

A package for detecting point-group symmetry for molecular systems.

Open-source cheminformatics toolkit for working with chemical informatics and molecular modeling

An open source method for structure generation, with or without conditional information (a motif, target etc).

A codebase that creates a new family of molecular dynamics programs that use shared C++ classes and GPU kernels to provide accessible, high-performance simulations across both CPU and GPU platforms with minimal performance trade-offs.

Tools for building polydisperse and crosslinked polymer systems for molecular dynamics.

End-To-End Molecular Dynamics (MD) Engine using PyTorch

A package for constructing and running stochastic simulations using the weighted ensemble approach for enhanced sampling of rare events.

An easy to use Python API for creating and deploying ADMET Models to AWS