Computational Large‐Scale Mapping of Protein‐Protein Interactions Using Structural Complexes
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- Abstract
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Abstract
Although the identification of protein interactions by high?throughput methods progresses at a fast pace, ?interactome? datasets still suffer from high rates of false positives and low coverage. To map the interactome of any organism, this unit presents a computational framework to predict protein?protein or gene?gene interactions utilizing experimentally determined evidence of structural complexes, atomic details of binding interfaces and evolutionary conservation. Curr. Protoc. Protein Sci . 73:3.9.1?3.9.9. © 2013 by John Wiley & Sons, Inc.
Keywords: protein interaction; structural complex; binding interface; IBIS; Inferred Biomolecular Interactions Server
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- Introduction
- Basic Protocol 1: Computational Prediction of Protein Interactions on the Organism Scale Using IBIS
- Commentary
- Literature Cited
- Figures
- Tables
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Figure 3.9.1 The biological rationale allowing the prediction of potential protein‐protein interactions from structural protein complexes with known binding sites. In the first step, protein complexes with known structures are collected. In the second step, a query protein sequence/structure is superimposed on or aligned with the homologous protein complexes. Assuming that an alignment covers a binding site of the known underlying protein structure, potential protein interaction partners are inferred from a homolog to a query protein. View Image -
Figure 3.9.2 Flowchart of the computational inference of protein interactions. View Image
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Literature Cited
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