Thursday, July 27, 2006

Protein-protein interactions from evolutionary information

Protein interactions are key for understanding the functions of genes and proteins.

Multiple sequence alignments are rich sources of evolutionary information: conserved positions in structural cores and active sites; family-dependent conservation (tree determinants); coevolution (correlated mutations).

Sequence-based methods for prediction of interacting regions
  • Tree-Determinant Residues and interacting surfaces,
  • Correlated mutations: can point to the residues and regions implicated in the interaction between the two proteins,
Hybrid methods use both structure (docking) and sequence information: neural networks.

Computational methods based on genomic information:
  • Phlyogenetic Profiles,
  • Conservation of Gene Neighboring,
  • Gene Fusion: related to presence of fused genes in various genomes,
Computational methods based on sequence information:
  • Correlated Mutations (i2h),
  • Similarity of Phylogenetic Trees (mirrortree).

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