ZhangGroup-MITChemistry

Pinned Repositories

chromVAE
variational autoencoder used to analyze chromatin imaging data
Language:Jupyter Notebook4 3 03
DiploidGenomeOrganization
Language:C++4 2 00
DRAGON
Language:Python11 4 01
ELP
Code to calculate the surface tension and micropolarity from multiscale simulations of ELP condensates
Language:Python1 3 00
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)
Language:Python9 4 03
MOFF-IDP
Language:Python2 2 00
OpenABC
OpenMM implementation of MOFF, MRG-CG, and HPS models.
Language:Python24 2 14
OpenNucleome
Language:Jupyter Notebook13 1 10
PCCG
Potential Contrasting Coarse-Graining
Language:Python9 3 00
tetra-nucl-msm
Language:Roff1 3 00

ZhangGroup-MITChemistry's Repositories

ZhangGroup-MITChemistry/OpenABC
OpenMM implementation of MOFF, MRG-CG, and HPS models.
Language:Python24 2 14
ZhangGroup-MITChemistry/OpenNucleome
Language:Jupyter Notebook13 1 10
ZhangGroup-MITChemistry/DRAGON
Language:Python11 4 01
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)
Language:Python9 4 03
ZhangGroup-MITChemistry/PCCG
Potential Contrasting Coarse-Graining
Language:Python9 3 00
ZhangGroup-MITChemistry/chromVAE
variational autoencoder used to analyze chromatin imaging data
Language:Jupyter Notebook4 3 03
ZhangGroup-MITChemistry/DiploidGenomeOrganization
Language:C++4 2 00
ZhangGroup-MITChemistry/MOFF-IDP
Language:Python2 2 00
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.
Language:C++1 1 00
ZhangGroup-MITChemistry/ELP
Code to calculate the surface tension and micropolarity from multiscale simulations of ELP condensates
Language:Python1 3 00
ZhangGroup-MITChemistry/NucleoliCoalescence
Language:C++1 4 01
ZhangGroup-MITChemistry/smog-3spn2-openmm
Language:Python1 2 01
ZhangGroup-MITChemistry/tetra-nucl-msm
Language:Roff1 3 00
ZhangGroup-MITChemistry/TetraNucl
Near-atomistic modeling of tetra-nucleosome
1 2 00
ZhangGroup-MITChemistry/AWSEM-parameters
0 1 00
ZhangGroup-MITChemistry/AWSEM-SAXS
Code to run AWSEM-SAXS simulations
Language:C++0 2 00
ZhangGroup-MITChemistry/CodeDynPTChrXHist
Language:Cython0 4 00
ZhangGroup-MITChemistry/brd2-reanalysis
Language:Jupyter Notebook4 0
ZhangGroup-MITChemistry/Compartmentalization_Nuclear_Landmarks
Language:C++3 0
ZhangGroup-MITChemistry/Explicit_Ion_Chromatin
Lammps Implementation of the Explicit-ion Residue-resolution Chromatin Model
Language:C++4 01