SCALI : Structural Core ALIgnment of proteins

SCALI alignment example

Nonsequential Protein Structure Alignments

Upload and align two PDB files:

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PDB file 1 Chain
PDB file 2 Chain
Standard sequential alignment ...or non-sequential   

Browse the structure aligment database
Download and install SCALI software (unix only)
Read about SCALI structure-based alignments
Please cite: Yuan X, and Bystroff C.(2005) "Non-sequential Structure-based Alignments Reveal Topology-independent Core Packing Arrangements in Proteins", Bioinformatics. 27(7):1010-1019 [Nov 5, 2004; Epub]
Contacts: Chris Bystroff:; Xin (Jean) Yuan :

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Last updated Mon Mar 17 09:37:21 EDT 2014