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3D-SURFER 2.0

A web-based tool for real-time protein surface comparison and analysis. The server integrates a repertoire of methods to assist in high throughput screening and visualization of protein surface comparisons. 3D-Zernike Descriptors (3DZD) are utilized for the efficient comparison between a protein surface of a single chain, a single domain, or a single complex against all protein structures in the latest Protein Data Bank (PDB). Conveniently, the web interface also renders animated protein rotations, displays CATH protein structure classification codes, and structure alignment calculations using the Combinatorial Extension (CE) algorithm, and identifies geometric (i.e., pocket) regions on a given structure.

Statistics of latest release (Last updated on Oct 17, 2014):

All Entries 466,678
  Chain Entries 264,039
  Complex Entries 67,051
  Domain Entries 135,588
All (CACN) Entries 467,310
  Chain (CACN) Entries 264,496
  Complex (CACN) Entries 67,074
  Domain (CACN) Entries 135,740
 

 

Latest features:

  • Surface representation:Two options of surface representation are provided. The first one is the all-atom-surface representation, and the second is the backbone-atom-surface representation, which includes alpha C (CA), C, and N atoms in the main chain.

  • Database:3DZD of protein chains, domains, complexes and a combination of three above are repertoried in the website.

  • Batch mode: A batch mode is available to run multiple proteins for uses who would like to benchmark their methods against our approach.

  • Maintenance: The databases are weekly updated in pace with the latest PDB.


   
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