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    22 repositories

    • Schake_GNN

      Public
      Multiscale Schake graph neural network for proteins
      Python
      •0•0•0•0•Updated Jan 21, 2025Jan 21, 2025

    • ChromoGen

      Public
      Jupyter Notebook
      •
      MIT License
      •0•12•0•0•Updated Dec 5, 2024Dec 5, 2024

    • OpenABC

      Public
      OpenMM implementation of MOFF, MRG-CG, and HPS models.
      Python
      •
      MIT License
      •6•27•3•1•Updated Sep 30, 2024Sep 30, 2024

    • tetra-nucl-msm

      Public
      Roff
      •0•1•0•0•Updated Jul 18, 2024Jul 18, 2024

    • CodeDynPTChrXHist

      Public
      Cython
      •0•0•0•0•Updated Apr 17, 2024Apr 17, 2024

    • Explicit_Ion_Chromatin

      Public
      Lammps Implementation of the Explicit-ion Residue-resolution Chromatin Model
      C++
      •
      MIT License
      •1•1•0•0•Updated Apr 6, 2024Apr 6, 2024

    • OpenNucleome

      Public
      Jupyter Notebook
      •
      MIT License
      •0•23•2•0•Updated Mar 27, 2024Mar 27, 2024

    • brd2-reanalysis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Feb 22, 2024Feb 22, 2024

    • ELP

      Public
      Code to calculate the surface tension and micropolarity from multiscale simulations of ELP condensates
      Python
      •
      MIT License
      •0•1•0•0•Updated Sep 6, 2023Sep 6, 2023

    • DRAGON

      Public
      genomicsmolecular-dynamics3d-genomeepigenomicschromatin-structure
      Python
      •
      GNU General Public License v3.0
      •1•12•0•0•Updated Jun 16, 2023Jun 16, 2023

    • smog-3spn2-openmm

      Public
      Python
      •
      MIT License
      •1•1•0•0•Updated May 3, 2023May 3, 2023

    • Compartmentalization_Nuclear_Landmarks

      Public
      C++
      •0•0•0•0•Updated Mar 19, 2023Mar 19, 2023

    • PCCG

      Public
      Potential Contrasting Coarse-Graining
      Python
      •
      MIT License
      •0•9•1•0•Updated Sep 28, 2022Sep 28, 2022

    • MOFF

      Public
      Implementation of MOFF force field. Please cite us at Latham, A; Zhang, B J. Chem. Theory Comput. 2021, 17, 3134. (https://pubs.acs.org/doi/abs/10.1021/acs.jctc.0c01220)
      Python
      •3•9•0•0•Updated Jun 16, 2022Jun 16, 2022

    • NucleoliCoalescence

      Public
      C++
      •
      GNU General Public License v2.0
      •1•1•0•0•Updated Nov 15, 2021Nov 15, 2021

    • TetraNucl

      Public
      Near-atomistic modeling of tetra-nucleosome
      0•1•0•0•Updated Jan 17, 2021Jan 17, 2021

    • DiploidGenomeOrganization

      Public
      C++
      •
      GNU General Public License v2.0
      •0•4•0•0•Updated Jan 13, 2021Jan 13, 2021

    • chromVAE

      Public
      variational autoencoder used to analyze chromatin imaging data
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•4•0•0•Updated Feb 7, 2020Feb 7, 2020

    • MOFF-IDP

      Public
      Python
      •0•2•0•0•Updated Dec 4, 2019Dec 4, 2019

    • AWSEM-SAXS

      Public
      Code to run AWSEM-SAXS simulations
      C++
      •0•0•0•0•Updated Dec 2, 2019Dec 2, 2019

    • Chrom_cluster

      Public
      This is the repository of the core scripts for the chromosome clustering project. It includes two individual folders, which is responsible for 1d extrusion and 3d MD simulation, respectively.
      C++
      •0•1•0•0•Updated Apr 22, 2019Apr 22, 2019

    • AWSEM-parameters

      Public
      0•0•0•0•Updated Oct 19, 2018Oct 19, 2018