In NDB user can find data for 3D genome structures and also computational tools for simulating the genome. The server is also made for visualization the structures and dynamics of the genome, allowing users to explore the 3D organization of chromosomes from their computer.
This platform enables users to visualize and annotate the 3D chromosome structures with experimental tracks from ENCODE or with their own data, allowing for an integrative experience for all genome scientists.
NDB uses a novel computational pipeline to create a physics-based model of individual chromosomes from chromatin immunoprecipitation input data. This physical model can be simulated using the GROMACS molecular dynamics package.
NDB also serves as a repository for simulation trajectories that have already been generated for various ENCODE cell lines.