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. 2008 Oct 6;14(1):1–22. doi: 10.2478/s11658-008-0024-7

The interactome: Predicting the protein-protein interactions in cells

Dariusz Plewczyński 1,✉, Krzysztof Ginalski 1
PMCID: PMC6275871  PMID: 18839074

Abstract

The term Interactome describes the set of all molecular interactions in cells, especially in the context of protein-protein interactions. These interactions are crucial for most cellular processes, so the full representation of the interaction repertoire is needed to understand the cell molecular machinery at the system biology level. In this short review, we compare various methods for predicting protein-protein interactions using sequence and structure information. The ultimate goal of those approaches is to present the complete methodology for the automatic selection of interaction partners using their amino acid sequences and/or three dimensional structures, if known. Apart from a description of each method, details of the software or web interface needed for high throughput prediction on the whole genome scale are also provided. The proposed validation of the theoretical methods using experimental data would be a better assessment of their accuracy.

Key words: Protein-protein interactions, Protein complexes, Docking, PDB Database, Interactome, Protein interaction networks, Physical protein interactions

Full Text

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Abbreviations used

3D

three dimensional

BIND

Biomolecular Interaction Network Database

BLAST

Basic Local Alignment Search Tool

CAPRI

Critical Assessment of PRediction of Interactions

DBID

database of interacting domains

DIP

Database of Interacting Proteins

DNA

deoxyribonucleic acid

GO

Gene Ontology

HPRD

Human Protein Reference Database

KEGG

Kyoto Encyclopedia of Genes and Genomes

KO

KEGG Orthology

MetaBASIC

Bilaterally Amplified Sequence Information Comparison

MINT

Molecular Interaction Database

OPHID

Online Predicted Human Interaction Database

PDB

Protein Data Bank

RNA

ribonucleic acid

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