Crescendo | User Guide | Theory Crystallography and Bioinformatics Group
University of Cambridge 
CRESCENDO  

 

Crescendo is a program which identifies functional sites in proteins. The conservation of amino acid residues has been shown to be strongly dependent on the environment in which they occur in the folded protein and this information is stored quantitatively in the form of environment specific substitution tables (ESSTs). An sequence alignment is used alongside a representative structure to identify those residues in the alignment that are more conserved than would be expected based on the local structural environment of the representative structure. This allows us to distinguish structural restraints on proteins from those restraints that arise from proteins interacting with other molecules i.e. functional restraints.

For more information please see the references listed below.

References

[1] Chelliah V, Chen L, Blundell TL, Lovell SC. (2004) Distinguishing structural and functional restraints in evolution in order to identify interaction sites. J Mol Biol. 342(5), 1487-504.

[2]Chelliah V, Blundell T, Mizuguchi K (2005) Functional restraints on the patterns of amino acid substitutions: application to sequence-structure homology recognition. Proteins61(4) 722-31.

[3] Chelliah V, Blundell TL (2005) Quantifying structural and functional restraints on amino acid substitutions in evolution of proteins. Biochemistry (Mosc). 70(8):835-40.

[3] Chelliah V, Blundell TL, Fernandez-Recio J (2006) Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment. J Mol Biol. 357(5):1669-82.