Structure Alignment View

Pre-calculated jFATCAT_rigid results for d3bmva4 vs. PDP:3DHUAa .

This page provides a summary view of the protein structure alignment.

Structure Alignment Results
Alignment Details: Query: (
orange/dark grey)
Cyclomaltodextrin glucanotransferase3bmv A:1-406 c.1.8.1 (Trans)glycosidases
Subject: (
cyan/light grey)
P-value: 1.56e-11
Score: 594.12
RMSD: 3.05
%Id: 15.0%
SCOP domain d3bmva4
Length: 406
Similarity: 79%
EC number:
PDP Domain: PDP:3DHUAa
Length: 338
Similarity: 95%
EC number:
Comparison Method
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d3bmva4 |

It is also possible to view this alignment using the stand-alone Java Web Start application.

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A detailed description of the procedure for the all vs. all alignments is available.

Algorithm: The alignment displayed on this page is based on the jFATCAT_rigid algorithm, a Java port of the original FATCAT algorithm.

Yuzhen Ye & Adam Godzik (2003)
Flexible structure alignment by chaining aligned fragment pairs allowing twists. 
Bioinformatics vol.19 suppl. 2. ii246-ii255.
[pdf  ]

RCSB PDB Comparison Tool Reference
Andreas Prlić; Spencer Bliven; Peter W. Rose; Wolfgang F. Bluhm; Chris Bizon; Adam Godzik; Philip E. Bourne (2010)
Pre-calculated protein structure alignments at the RCSB PDB website
Bioinformatics 26: 2983-2985

For more information on the algorithms see here.