Academic 3D genome resource

Nucleome Data Bank

A web platform to simulate, browse, visualize, and analyze the three-dimensional architecture of genomes.

Browse Data Visualize Structures

Repository 3D chromosomal structures

Download simulation trajectories and associated structural data for ENCODE cell lines.

Tools Open-MiChroM and TECSAS

Access scientific software resources for chromatin dynamics and structural annotation.

Platform

Explore genome structure from data to visualization

NDB combines physics-based models, curated trajectory downloads, and interactive visualization tools for genome scientists.

Download curated datasets

Find available chromosome structures, trajectory archives, and related data files through the searchable data interface.

Open Data

Inspect 3D structures

Use the browser-based viewer to select cell lines, chromosomes, representations, coloring, and highlighted ranges.

Open Visualization

Use scientific software

Connect NDB data with Open-MiChroM chromatin simulations and TECSAS structural annotations.

View Software

About NDB

Built for integrative 3D genome research

NDB provides data for 3D genome structures and computational tools for simulating the genome. The server supports visualization of chromosome structures and dynamics, including annotation with experimental tracks from ENCODE or user-provided data. NDB uses a computational pipeline to create physics-based models of individual chromosomes from chromatin immunoprecipitation input data, and serves as a repository for simulation trajectories generated for ENCODE cell lines.