Protein Shell::Core::Face Comparison Server

INTERPARE   The Protein Interfaceome Database

1. PSIMAP and its Algorithm



PSIMAP, the Protein Structural Interactome Map, is a database of all the structurally observed interactions among protein domains of known three-dimensional structures in the PDB.
It can be constructed using any reliable protein domain definition, where domains are defined as evolutionarily conserved structural and functional protein units. Here we use the domain definitions provided by SCOP (Structural Classification of Proteins), which uses structural and functional homology to manually define evolutionarily distinct protein domain families and superfamilies. Alternatively, other domain definitions (such as CATH, FSSP, Pfam, etc.) can be used.

Domains from a multi-domain PDB entry are empirically denoted as interacting with each other if at least 5 residue pairs are within a 5 Angstrom distance. Although the data in the PDB is relatively limited in comparison to the available sequence data, it is much more comprehensive when compared to the available protein interaction data.

PSIMAP provides an overview of all the observed domain-domain interactions at the protein family or superfamily level.
It is important to consider protein interactions at this level with respect to the stability of the network; while the number of PDB entries is growing superlinearly, the number of new folds is only increasing linearly. It is probable that there are no more than 2,000 distinct protein topologies in nature.

Because of the slow growth in the number of new superfamilies and superfamily interactions over time, PSIMAP represents the first global overview of interactions at this level.
For example, the recent conservative superfamily assignment of 56 genomes covered between 40-67% of the total detected genes in eukaryotes and eubacteria (~100,000 genes) and between 31-54% of the total detected genes in archaebacteria (~10,000 genes).

As a significant portion of the unassigned genes may represent trans-membrane proteins not structurally determined due to experimental difficulties, it is reasonable to suggest that the PDB and PSIMAP cover many of the existing globular superfamilies in nature.



Read more here.


Read about the concept and the assumptions of PSIMAP.


Visit PSIMAP database or PSIbase. 





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