What can I do with PDBe

Why do we need PDBe?

Structural biology continues to have an enormous impact on our understanding of biology and medicine. Three-dimensional structures give us insight into how macromolecules work, and help to explain how their functions are disrupted by mutation or by interaction with small molecules. Biologists are now in a position to combine structural biology with genomics approaches to determine every protein fold encoded by a genome. As these efforts gain momentum, the demand for efficient access to sequence, structure and protein-family information is rising; biologists need standardised ways of viewing and describing proteins so that they can share and use data effectively.

Figure 1 The PDBe homepage provides access to tools and services for depositing, searching, exploring and analysing macromolecular structural data.

PDBe services

Macromolecular structures are complex and therefore advanced tools are needed for their analysis. PDBe’s suite of web-based services allows you to make the most of the global collection of publicly available structural data.

PDBe Service Description

 

Access to PDB entries Get more information about PDB entry 1xyz.
Download PDB entry Download the PDB file of entry 1xyz (access from home page).
PDB Deposition Service Deposit data to the PDB using AutoDep.
PDBeView PDB search tool.
PDBeChem Dictionary of chemical components (ligands, small molecules and monomers) in the PDB. Search and visualise ligands using keywords, PDB codes, SMILES strings, fragments or fingerprints.
PDBeXplore Browse, list and analyse the structural knowledge embodied in the PDB based on classification systems that are familiar and intuitive to molecular biologists, biochemists and other life scientists.
PDBeMotif Query and analysis of ligands, sequence and structure motifs, their relative position and the neighbouring environment.
PDBePisa Search and analysis of protein interfaces, surfaces and assemblies. Can be used to predict probable quarternary structures (assemblies).
PDBeFold Secondary Structure Matching (SSM) service for comparing and aligning 3D protein structures; search for structures that are similar to that of a reference protein, and visualise superimposed structures.
SIFTS

The Structure Integration with Function, Taxonomy and Sequence (SIFTS) resource provides up-to-date mappings between macromolecular structures and other major bioinformatics resources.

NMR at PDBe Access the NMR project pages at PDBe.
EM Data Bank Access the EM Data Bank pages at PDBe.
BioBar A downloadable toolbar for Mozilla browsers, providing instant access to PDBe and many other freely available bioinformatics services.

PDBe Services: at a glance

Analysing data in PDBe

Figure 2 Some of the ways in which PDBe’s services can be used to analyse structural data