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alchemiscale
Repo Docs Website
Licenses: MIT

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

Cloud ComputingFree EnergyHPCPython
BioEmu
Licenses: MIT

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.

Machine LearningMolecular DynamicsPython
Biotite
Repo Docs Website
Licenses: BSD-3

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.

BioinformaticsPython
cinnabar
Repo Docs Website
Licenses: MIT

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

AtomisticVisualizationStatistical AnalysisFree EnergyPython
exorcist
Repo Docs Website
Licenses: MIT

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

AtomisticSimulation OrchestrationData AnalysisPython
feflow
Repo Docs Website
Licenses: MIT

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

AtomisticFree EnergyComputational ChemistryMolecular DynamicsPython
ForceBalance
Licenses: BSD-3 Non-AI

Systematic force field optimization

Force Field OptimizationMolecular SimulationPython
Foyer
Repo Docs
Licenses: MIT

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

Force FieldsOPLS-AAGAFFAtom TyperPython
GMSO
Repo Docs
Licenses: MIT

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

GROMACSLAMMPSHOOMD-BlueCassandraGOMCParmEdPython
GROMACS
Repo Docs Website
Licenses: LGPL

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

Molecular DynamicsTrajectory AnalysisC++C
gufe
Repo Docs Website
Licenses: MIT

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

AtomisticFree EnergySimulation OrchestrationComputational ChemistryPython
Kartograf
Repo Docs Website
Licenses: MIT

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

VisualizationAtom Mapping3D GeometryHybrid-Topology SystemsPython
knuckles-rs
Repo Docs
Licenses: MIT

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

PDBRustPython
Konnektor
Repo Docs Website
Licenses: MIT

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

Graph TheoryAtomisticFree EnergyVisualizationNetwork PlanningPython
LAMMPS
Repo Docs Website
Licenses: GPL-2.0

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

Molecular DynamicsC++
mBuild
Repo Docs
Licenses: MIT

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

Molecular DynamicsMolecule InitializationBox PackingPolymer BuilderPython
MDAnalysis
Repo Docs Website
Licenses: LGPL

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Molecular Dynamics AnalysisTrajectory AnalysisMolecular Simulation Data HandlingC++PythonC
MDTraj
Repo Docs Website
Licenses: LGPL

An open library for the analysis of molecular dynamics trajectories

Molecular DynamicsAnalysisBiophysicsPythonC++
Molly
Repo Docs Website
Licenses: MIT

Molecular simulation in Julia

Molecular DynamicsMolecular SimulationForce Field OptimizationDifferentiableJulia
NAMD
Repo Docs Website
Licenses: University of Illinois/NCSA Open Source Proprietary

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

Molecular DynamicsLarge-scale simulationC++
NGLView
Repo Docs
Licenses: MIT

IPython/Jupyter widget to interactively view molecular structures and trajectories

JupyterIPythonMolecular VisualizationWebGLPythonJavaScriptHTMLCSS
openfe
Repo Docs Website
Licenses: MIT

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.

Free EnergyMolecular DynamicsPython
openff-bespokefit
Repo Docs Website
Licenses: MIT

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.

Bespoke Parameter CreationSMIRNOFF FormatParameterizationPython
openff-evaluator
Repo Docs Website
Licenses: MIT

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

Molecular DynamicsPhysical Property EstimationPython
openff-forcefields
Repo Docs Website
Licenses: CC-BY-4.0

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

Force FieldsSMIRNOFF FormatMolecular DynamicsPython
openff-fragmenter
Repo Docs Website
Licenses: MIT

A package for fragmenting molecules for quantum mechanics torsion scans.

Molecular FragmentationQuantum ChemistryTorsion ScansVisualizationPython
openff-interchange
Repo Docs Website
Licenses: MIT

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

Data ManipulationForce FieldsParametrizationPython
openff-nagl
Repo Docs Website
Licenses: MIT

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.

Force FieldsMachine LearningPython
openff-nagl-models
Repo Docs Website
Licenses: CC-BY-4.0

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

ParameterizationMachine LearningQuantum ChemistryPython
openff-qcsubmit
Repo Docs Website
Licenses: MIT

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

Quantum ChemistryPython
openff-recharge
Repo Docs Website
Licenses: MIT

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.

Quantum ChemistryPartial Charge AssignmentMachine LearningPython
openff-toolkit
Repo Docs Website
Licenses: MIT

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

Force FieldsMolecular DynamicsPython
openff-units
Repo Docs Website
Licenses: MIT

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

UnitsPython
openff-utilities
Licenses: MIT

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

Utility FunctionsPython
OpenFold (Monomer, Multimer and Soloseq)
Repo Docs Website
Licenses: Apache 2.0

A trainable PyTorch reproduction of DeepMind's AlphaFold2.

Protein FoldingAlphaFold2Structural BiologyDeep LearningComputational BiologyPython
OpenMM
Repo Docs Website
Licenses: MIT LGPL

High-performance toolkit for molecular simulation

Molecular DynamicsGPU AccelerationComputational ChemistryC++Python
Packmol
Repo Docs
Licenses: MIT

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

Molecular DynamicsMolecular PackingConfiguration GenerationFortran
ProteinMPNN
Licenses: MIT

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.

Deep LearningProtein Sequence DesignPython
Psi4
Repo Docs Website
Licenses: LGPL

An open-source ab initio quantum chemistry software package

Quantum ChemistryElectronic StructureAb Initio MethodsC++Python
RDKit
Repo Docs Website
Licenses: BSD-3

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

CheminformaticsMolecular ModelingC++Python
RFDiffusion
Licenses: BSD-3

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

Structure GenerationMotif ScaffoldingBinder designPython
STORMM
Repo Docs Website
Licenses: MIT

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.

Molecular DynamicsGPUHigh PerfomanceC++
WESTPA
Repo Docs Website
Licenses: MIT

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

Weighted EnsembleMolecular DynamicsEnhanced SamplingRare EventsStochastic SimulationPython