Following is a list of software developed by the group for studying genome structures. Check our GitHub for more information.
DRAGON is a software package to enable De novo, and RAtional prediction of Genome organizatiON. It provides a method to simulate chromatin structure and dynamics, described in PLOS Comp Biol. With DRAGON, one can predict cell type specific chromosome structures using genome-wide profiles of histone modifications and CTCF molecules.
The associative memory, water mediated, structure and energy model (AWSEM) has been widely used to model protein interactions. Our lab has applied this method to model nucleosome structure and to study nucleosome unwinding, described in J Chem Phys.
The maximum entropy optimized force field for IDPs (MOFF-IDP) was parameterized to more accurately reproduce the radius of gyration for a variety of disordered sequences, as shown in J. Chem. Theory Comput.
AWSEM with small angle X-ray scattering (SAXS) utilizes maximum entropy techniques to create minimially biased molecular dynamics simulations that recreate experimental SAXS profiles. This methodology, introduced in J. Phys. Chem. B, improves modeling of protein structure and conformational fluctation for proteins where SAXS data are available.