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Project Protein Dynamic Alignments
Project Name: Protein Dynamic Alignments
Project Start Date: 2009/05/01
Collaborators: Jordi Villà i Freixa [email protected], Raul E Alcantara [email protected], Carsten, Thomas, Cedric
Description :
Identification of functional activity and responsible sequence sites of a protein (family) using molecular dynamics and sequence alignments.
The output of molecular dynamic simulation of alpha-carbon atom movement ("Eigenmodes") is stretched according to a structure-guided multiple sequence alignment of the corresponding residues. Several Eigenmodes of different sequences are combined into "cliques" of well-matching Eigenmodes according to a greedy strategy using cumulative pairwise Eigenmode similarity.
The cliques can be used to build trees based on Eigenmode distance and to iteratively refine the initial sequence alignment using Eigenmode properties.
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