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The interactome: Predicting the protein-protein interactions in cells

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.

Abbreviations

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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Plewczyński, D., Ginalski, K. The interactome: Predicting the protein-protein interactions in cells. Cell Mol Biol Lett 14, 1–22 (2009). https://doi.org/10.2478/s11658-008-0024-7

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Key words

  • Protein-protein interactions
  • Protein complexes
  • Docking
  • PDB Database
  • Interactome
  • Protein interaction networks
  • Physical protein interactions