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    28 repositories

    • flexibletopology

      Public
      ML-based molecular representation models using PyTorch
      Python
      •
      MIT License
      •3•16•2•0•Updated Feb 25, 2026Feb 25, 2026

    • mlforce_ft

      Public
      C++
      •0•2•1•1•Updated Feb 19, 2026Feb 19, 2026

    • OpenRXN

      Public
      A free, open-source tool for modeling chemical reaction networks in Python
      reactionsreaction-diffusionpharmacokineticsgillespiegillespie-algorithmcompartmental-models
      Python
      •
      MIT License
      •3•13•0•2•Updated Feb 19, 2026Feb 19, 2026

    • wepy

      Public
      Weighted Ensemble simulation framework in Python
      simulationmolecular-dynamicsenhanced-samplingweighted-ensemble
      Python
      •
      MIT License
      •22•60•34•2•Updated Jan 22, 2026Jan 22, 2026

    • wepy-analysis

      Public
      Analysis tools for wepy simulations
      Python
      •
      MIT License
      •1•1•0•0•Updated Jul 31, 2025Jul 31, 2025

    • geomm

      Public
      Mirror of main geomm repository. Simple and stupid library for strictly geometric operations (zero-knowledge of topology) common to computational biology and ch…
      Python
      •
      MIT License
      •0•4•0•7•Updated Jul 7, 2025Jul 7, 2025

    • AGDIFF

      Public
      Implementation of AGDIFF: Attention-Enhanced Diffusion for Molecular Geometry Prediction
      machine-learningstructureattentionconformergraph-neural-networksgnndiffusion-modelsgenerative-ai
      Python
      •
      MIT License
      •0•16•0•0•Updated Jun 19, 2025Jun 19, 2025

    • openmmcontinuityforce

      Public
      An OpenMM force that ensures a set of atoms stay continuously connected in space
      C++
      •21•1•0•0•Updated Jun 11, 2025Jun 11, 2025

    • ClassicalGSG

      Public
      A new logP predictor method using GSG and NNs
      neural-networkslogpgeommetric-scattering-for-graphs
      Python
      •
      MIT License
      •1•9•1•0•Updated Oct 12, 2023Oct 12, 2023

    • openmm_systems

      Public
      Collection of premade molecular systems for use with OpenMM
      Python
      •
      MIT License
      •0•3•0•5•Updated Dec 8, 2022Dec 8, 2022

    • CSNAnalysis

      Public
      Tools for creating, analyzing and visualizing Conformation Space Networks
      Python
      •
      MIT License
      •3•17•2•0•Updated Aug 31, 2022Aug 31, 2022

    • mlforce

      Public
      A PyTorch OpenMM plugin to generate forces for Flexible Topology simulations
      C++
      •1•5•0•0•Updated May 15, 2022May 15, 2022

    • ml4md-jb

      Public
      Jupyter book and content for "Machine Learning for Molecular Dynamics" course
      Jupyter Notebook
      •3•13•0•0•Updated Apr 7, 2022Apr 7, 2022

    • wepy-activity

      Public
      This package is for use with Wepy. It can be used to calculate (un)binding free energies from pulling trajectories of Lennard-Jones Pairs. This also serves as a…
      Python
      •0•0•0•0•Updated Aug 16, 2020Aug 16, 2020

    • wepy-developer-resources

      Public
      Resources to support users and developers in the wepy ecosystem
      Python
      •0•0•0•0•Updated May 6, 2020May 6, 2020

    • staged-recipes

      Public
      A place to submit conda recipes before they become fully fledged conda-forge feedstocks
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5.8k•0•0•0•Updated Feb 1, 2020Feb 1, 2020

    • conda-recipes

      Public
      conda build recipes for the Omnia project
      Python
      •
      MIT License
      •37•0•0•0•Updated Jan 29, 2020Jan 29, 2020

    • WESTPA-WExplore

      Public
      A plugin to run the WExplore algorithm in the WESTPA toolkit
      Python
      •
      GNU General Public License v3.0
      •3•1•1•1•Updated Dec 16, 2019Dec 16, 2019

    • wepy-tests

      Public
      0•0•0•0•Updated Nov 4, 2019Nov 4, 2019

    • preprints

      Public
      0•0•0•0•Updated Jul 10, 2018Jul 10, 2018

    • openmmexampleplugin

      Public
      An example of how to write a plugin for OpenMM
      C++
      •21•0•0•0•Updated Mar 17, 2018Mar 17, 2018

    • pbvs_schrodinger

      Public
      Shell
      •3•0•0•0•Updated Jan 30, 2018Jan 30, 2018

    • mastic

      Public
      Multi-Atom Structure/Selection Toolkit with Interaction Capabilities
      protein-structurecomputational-biologycomputational-chemistryprotein-ligand-interactions
      Python
      •
      MIT License
      •1•10•0•0•Updated Jan 28, 2018Jan 28, 2018

    • scoop

      Public
      SCOOP (Scalable COncurrent Operations in Python)
      Python
      •
      GNU Lesser General Public License v3.0
      •87•0•0•0•Updated Jun 27, 2017Jun 27, 2017

    • LaTeX-Glossary

      Public
      A collection of some glossary and acronym entries for the glossaries LaTeX package
      TeX
      •
      Other
      •1•0•0•0•Updated Jun 6, 2017Jun 6, 2017

    • vmd_inxplot

      Public
      Collection of scripts for visualizing interactions in VMD
      Tcl
      •0•0•0•0•Updated Apr 27, 2017Apr 27, 2017

    • westpa

      Public
      WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
      Python
      •
      GNU General Public License v3.0
      •61•0•0•0•Updated Oct 10, 2016Oct 10, 2016

    • jekyll-ion-site

      Public
      Code to build lab website using jekyll with the "ion" theme
      CSS
      •
      Other
      •0•0•0•0•Updated Aug 8, 2016Aug 8, 2016