Pinned Repositories
chromVAE
variational autoencoder used to analyze chromatin imaging data
DiploidGenomeOrganization
DRAGON
ELP
Code to calculate the surface tension and micropolarity from multiscale simulations of ELP condensates
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
OpenABC
OpenMM implementation of MOFF, MRG-CG, and HPS models.
OpenNucleome
PCCG
Potential Contrasting Coarse-Graining
tetra-nucl-msm
ZhangGroup-MITChemistry's Repositories
ZhangGroup-MITChemistry/OpenABC
OpenMM implementation of MOFF, MRG-CG, and HPS models.
ZhangGroup-MITChemistry/OpenNucleome
ZhangGroup-MITChemistry/DRAGON
ZhangGroup-MITChemistry/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)
ZhangGroup-MITChemistry/PCCG
Potential Contrasting Coarse-Graining
ZhangGroup-MITChemistry/chromVAE
variational autoencoder used to analyze chromatin imaging data
ZhangGroup-MITChemistry/DiploidGenomeOrganization
ZhangGroup-MITChemistry/MOFF-IDP
ZhangGroup-MITChemistry/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.
ZhangGroup-MITChemistry/ELP
Code to calculate the surface tension and micropolarity from multiscale simulations of ELP condensates
ZhangGroup-MITChemistry/NucleoliCoalescence
ZhangGroup-MITChemistry/smog-3spn2-openmm
ZhangGroup-MITChemistry/tetra-nucl-msm
ZhangGroup-MITChemistry/TetraNucl
Near-atomistic modeling of tetra-nucleosome
ZhangGroup-MITChemistry/AWSEM-parameters
ZhangGroup-MITChemistry/AWSEM-SAXS
Code to run AWSEM-SAXS simulations
ZhangGroup-MITChemistry/CodeDynPTChrXHist
ZhangGroup-MITChemistry/brd2-reanalysis
ZhangGroup-MITChemistry/Compartmentalization_Nuclear_Landmarks
ZhangGroup-MITChemistry/Explicit_Ion_Chromatin
Lammps Implementation of the Explicit-ion Residue-resolution Chromatin Model