PDB-Explorer: a web-based interactive map of the protein data bank in shape space.

ABSTRACT:

Background

The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited.

Methods

A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as viru

SUBMITTER: Jin X 

PROVIDER: S-EPMC4619230 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature