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Computational Intelligence and Pattern Analysis in Biological Informatics by Jason T. Wang, Sanghamitra Bandyopadhyay, Ujjwal Maulik

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CHAPTER 15

PREDICTION OF PROTEIN–PROTEIN INTERACTIONS

ANGSHUMAN BAGCHI

15.1 INTRODUCTION

Protein–protein interactions (PPI) play a major role in many biological processes e.g., hormone receptor binding, protease inhibition, antigen–antibody interactions, signal transduction, chaperone activity, enzyme allostery, to name a few [1–8]. The associations of proteins may be transient or permanent. The interfaces of the interacting proteins have specific different characteristics. The identification of the interface residues may shed light on many important aspects, like drug development, elucidation of molecular pathways, generation of protein mimetics, and understanding of disease mechanisms, as well as development of docking methodologies to build structural models of protein complexes. Before going into the details of the various PPI prediction methodologies, a few basic definitions, which are frequently used in the analysis of PPIs, need to be introduced.

15.2 BASIC DEFINITIONS [9, 10]

Monomer. A single unit of an assembly.

Polymer. An assembly of single monomeric units [i.e., Polymer = (Monomer)n].

If n = 2, the polymer is called a dimer

If n = 3, the polymer is called trimer, and so on.

Protomer. The monomeric constituent units of a protein having two or more monomeric protein chains.

Homomer. A protein with same monomeric constituents.

Heteromer. A protein with different monomeric constituents.

Obligate and Nonobligate Protein–Protein Complexes. A protein–protein complex where ...

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