PCFamily, PPISearch and 3D-partner: Systems Biology

We derive a new concept, called the 3D-domain interologswhich is similar to interologs.

The 3D-domain interologs is defined as Domain a (in chain A) interacts with domain b (in chain B) in a known 3D complex, their inferring protein pair A' (containing domain a ) and B' (containing domain b ) in the same species would be likely to interact with each other if both protein pairs (A' and A as well as proteins B and B') are homologous.

3D-partner (3D-partner: a web server to infer interacting partners and binding models) and PCFamily, published in Nucleic Acids Research, predicts interacting partners and binding models by using3D-domain interologs through structure complexes and a knowledge-based scoring function. These homologous structures and interacting partners were evaluated by a new scoring function which considered steric and special-bond matrices but also the interfacial stability (couple-conserved residue score and template similarity).

Protein-Protein-Interaction

  • (PS)2 : Protein Structure Prediction Server

  • PCFamily : Protein Complex Family Search

  • PPIsearch : Protein-Protein Interaction Search

  • 3D-partner : Discovery protein interaction partner

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