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awsem-parameters

awsem-saxs

Code to run AWSEM-SAXS simulations

brd2-reanalysis

chrom_cluster

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.

chromvae

variational autoencoder used to analyze chromatin imaging data

codedynptchrxhist

compartmentalization_nuclear_landmarks

diploidgenomeorganization

dragon

elp

Code to calculate the surface tension and micropolarity from multiscale simulations of ELP condensates

explicit_ion_chromatin

Lammps Implementation of the Explicit-ion Residue-resolution Chromatin Model

moff

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)

moff-idp

nucleolicoalescence

openabc

OpenMM implementation of MOFF, MRG-CG, and HPS models.

opennucleome

pccg

Potential Contrasting Coarse-Graining

smog-3spn2-openmm

tetra-nucl-msm

tetranucl

Near-atomistic modeling of tetra-nucleosome