Title

A computational tool for identifying minimotifs in protein-protein interactions and improving the accuracy of minimotif predictions.

Document Type

Article

Abstract

Protein-protein interactions are important to understanding cell functions; however, our theoretical understanding is limited. There is a general discontinuity between the well-accepted physical and chemical forces that drive protein-protein interactions and the large collections of identified protein-protein interactions in various databases. Minimotifs are short functional peptide sequences that provide a basis to bridge this gap in knowledge. However, there is no systematic way to study minimotifs in the context of protein-protein interactions or vice versa. Here we have engineered a set of algorithms that can be used to identify minimotifs in known protein-protein interactions and implemented this for use by scientists in Minimotif Miner. By globally testing these algorithms on verified data and on 100 individual proteins as test cases, we demonstrate the utility of these new computation tools. This tool also can be used to reduce false-positive predictions in the discovery of novel minimotifs. The statistical significance of these algorithms is demonstrated by an ROC analysis (P = 0.001).

Keywords

Algorithms; Amino acid sequence; Animals; Cell physiology; Computer simulation; Databases; Protein; GRB2 Adaptor Protein/chemistry; HomoloGene; Humans; Insect Proteins/chemistry; Mice; Minimotif Miner; Models; Molecular; Protein binding; Protein Interaction Domains and Motifs; Protein Interaction Mapping; Proteins/chemistry; Protein-protein interactions; Rats; SLiM; Short Linear Motifs; Software

Disciplines

Computer Sciences | Life Sciences | Molecular Biology | Structural Biology

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