Protein Structure Alignment by TOPOFIT

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a comprehensive database of accurate protein structure alignments by TOPOFIT

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Protein Structure Alignment Database TOPOFIT-DB
contains structural alignments between all proteins in the PDB. Last update: Feb 2011, see Statistics .

Structural neighbors to the query protein structure can be retrieved by the PDB code and chain id. Pairwise or multiple structural alignments can be visualized in 3D with the FRIEND software .

To find structural realtions with your protein, please submit its PDB code, (for example: 1rnt ) and, if you know, its chain letter, otherwise left chain blank

PDB-code chain 

Show only Centroids in Results
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or Enter SCOP/ASTRAL domain codes

**Add additional parameters
show     results with Z-Score 
and   RMSD and     length difference
and sort them by  
and   show additional values

(T-DB pages are under construction, any comments are welcome). (example output)
TOPOFIT-DB web link:
TOPOFIT-DB Reference: Chesley M.Leslin, Alexej Abyzov, and Valentin A. Ilyin, TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. Nucleic Acids Research 2007 35(Database issue):D317-D321

TOPOFIT Reference: Valentin A. Ilyin, Alexej Abyzov, and Chesley M.Leslin, Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point. Protein Science (2004), 13:1865-1874.

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Friday 18th 2014f April 2014 03:19:01 AM