Structure Alignment View

Pre-calculated jCE results for d4hhba_ vs. d4hhbb_ .

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

Structure Alignment Results
Alignment Details: Query: (
orange/dark grey)
HEMOGLOBIN (DEOXY) (ALPHA CHAIN)4hhb A: a.1.1.2 Globin-like
Subject: (
cyan/light grey)
HEMOGLOBIN (DEOXY) (BETA CHAIN)4hhb B: a.1.1.2 Globin-like
Z-score: 6.47
Score: 366.29
RMSD: 1.49
%Id: 40.8%
SCOP domain d4hhba_
Length: 141
Similarity: 99%
EC number:
SCOP domain d4hhbb_
Length: 146
Similarity: 95%
EC number:
Comparison Method
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Color Legend
d4hhba_ |

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 jCE algorithm, a Java port of the original Combinatorial Extension (CE) algorithm. (Implementation by Andreas Prlić).

I.N. Shindyalov, P.E. Bourne (1998)
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. 
Protein Eng 11: 739-747
[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.