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Scindices / openmm--openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

status-active lang-python lang-cpp role-framework entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-physics domain-molecular-simulation entity-trajectory interface-gpu lang-cuda ecosystem-openmm task-md-engine

Updated Jul 27, 2026
C++

Scindices / openforcefield--openff-toolkit

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The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

status-active lang-python domain-cheminformatics method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda method-physics domain-molecular-simulation role-toolkit scope-suite task-parameterization ecosystem-rdkit task-forcefield ecosystem-openff

Updated Jul 27, 2026
Python

Scindices / molssi-seamm--molsystem

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Molsystem provides a general class for handling molecular and periodic systems

status-active role-library lang-python domain-cheminformatics method-chemoinformatics entity-protein entity-small-molecule interface-api status-published status-packaged-pypi scope-focused method-physics domain-molecular-simulation task-system-model entity-crystal

Updated Jun 30, 2026
Python

Scindices / rlabduke--reduce

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Reduce - tool for adding and correcting hydrogens in PDB files

status-active lang-cpp interface-cli role-application domain-structural-biology entity-protein status-published status-packaged-conda scope-focused method-physics entity-nucleic-acid task-structure-prep method-rule-based

Updated Jan 5, 2026
C++

Scindices / openforcefield--openff-forcefields

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Force fields produced by the Open Force Field Initiative

status-active lang-python entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda method-physics domain-molecular-simulation scope-suite task-forcefield ecosystem-openff role-dataset

Updated Jul 6, 2026
Python

Scindices / RBVI--ChimeraX

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Source code for molecular graphics program UCSF ChimeraX

status-active lang-python lang-cpp task-visualization interface-cli domain-structural-biology task-file-io task-structure-analysis method-chemoinformatics entity-protein entity-small-molecule interface-api status-published method-physics entity-complex scope-swissknife entity-nucleic-acid interface-gui role-viewer

Updated Jul 29, 2026
Python

Scindices / torchmd--torchmd

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

status-active lang-python method-deep-learning role-framework entity-small-molecule interface-api status-published status-packaged-pypi scope-focused method-physics domain-molecular-simulation entity-trajectory interface-gpu task-md-engine task-ml-potential

Updated Apr 21, 2026
Python

Scindices / durrantlab--POVME

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Detect and characterize binding pockets from molecular simulations.

status-active lang-python interface-cli role-application entity-protein interface-api status-published scope-focused domain-drug-discovery task-pocket-detection method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory

Updated Mar 17, 2026
Python

Scindices / ccsb-scripps--AutoDock-Vina

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AutoDock Vina

status-active lang-cpp interface-cli role-application domain-structural-biology entity-protein entity-small-molecule status-published status-packaged-conda scope-focused domain-drug-discovery task-docking method-physics entity-complex ecosystem-autodock

Updated Feb 25, 2026
C++

Scindices / ccsb-scripps--AutoGrid

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status-archived lang-c interface-cli role-application domain-structural-biology entity-protein entity-small-molecule status-published scope-focused domain-drug-discovery task-docking method-physics ecosystem-autodock task-featurization

Updated Dec 7, 2024
C++

Scindices / OpenFreeEnergy--openfe

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The Open Free Energy toolkit

status-active lang-python interface-cli role-framework entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda domain-drug-discovery method-physics entity-complex method-statistics domain-molecular-simulation scope-suite ecosystem-openmm task-free-energy ecosystem-openfe

Updated Jul 29, 2026
Python

Scindices / AngelRuizMoreno--Jupyter_Dock

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Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

lang-python status-archived task-visualization role-application domain-structural-biology method-chemoinformatics entity-protein entity-small-molecule interface-jupyter status-published scope-focused domain-drug-discovery task-docking method-physics entity-complex

Updated Oct 30, 2023
Jupyter Notebook

Scindices / KurtzmanLab--SSTMap

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Solvation Structure and Thermodynamic Mapping

status-active lang-python lang-cpp interface-cli role-application entity-protein interface-api status-published scope-focused domain-drug-discovery method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory task-free-energy

Updated Dec 17, 2025
Python

Scindices / POVME--POVME3

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A pocket volume analyzer for use in protein modeling.

lang-python status-archived interface-cli role-application domain-structural-biology entity-protein interface-api status-published status-packaged-pypi scope-focused domain-drug-discovery task-pocket-detection method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory

Updated Oct 2, 2022
Python

Scindices / Discngine--fpocket

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fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software.