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.

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The Accessible Surface Area (ASA) method detects protein regions that are buried to be excluded from a solvent when forming a multimer or a complex. If more than two subunits interact or aggregate with each other, they lose some area that could be accessible by a solvent in the state of free subunit or domain.

In the InterPare method, we define residues as interface residues if they lost more than 1Ų solvent accessible surface area (ASA) on aggregation or complexation (Jones et al., 1996, 1997, 2000). The ASA of protein molecules was calculated using a program called NACCESS (Hubbard S., http://wolf.bms.umist.ac.uk/naccess) which is an implementation of the algorithm developed by Lee and Richards (Lee et al., 1971). It calculates the absolute ASA and the relevant ASA in terms of total residues, side chains, polar atoms, and non-polar atoms.

Relative accessibilities are calculated for each amino acid in the protein by expressing the summed residue accessible surface as a percentage of that observed in an ALA-X-ALA tri-peptide (Hubbard et al., 1991). Surface residues are defined as those residues that had a relative ASA of more than 5% (Miller et al., 1987). Interior residues are defined as those residues that have a relative ASA of less than 5%. The default van der Waals radii of atoms were taken from Chothia (Chothia, 1976). We used water of 1.40 van der Waals radii as a solvent.

The Voronoi diagram, known as Dirichlet tessellation, has been widely used in the fields of science and engineering. The Voronoi diagram was first introduced as an application to the study of protein structure by Richards et al. (1974, 1977).

There is a report on defining molecular interfaces by Power Diagram - Voronoi Diagram on weighted points set (Varshney et al., 1995). We used the same protocol suggested by Varshney et al., except for two aspects.

First, we did not use polygon filtering by distance threshold in that we already had interfaces defined by distance threshold method.

Second, we calculated interfaces on domains instead of calculating them on protein complexes. We first constructed a three dimensional power-diagram P of the atoms. The construction of such a power diagram will have a time complexity of (n is number of atoms in the protein) where the number of neighbors for any given atom is bounded by a constant.

Each face of the power-diagram P is defined by two atoms (Figure 3). For each face in P, if two atoms defining a face belong to different domains from each other, we call such face as interface face. Let us define interface-cell as a cell in the power-diagram P that has at least one interface-face. Let us define interface-atoms to be those atoms whose cells are interface-cells.

In the InterPare database, all the interface-atoms between two domain pairs are stored in a PDB-style file format. The default van der Waals radii of atoms were taken from Chothia (1976).