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Many protein-protein interactions involved in signal transduction occur through the interaction of modular protein domains in one molecule with short linear sequences of amino acids ("motifs") in another. Although protein domains are recognized by a variety of computational tools, bioinformatic approaches alone have not been successful in identifying the short sequence motifs to which domains bind. A new approach, applying motif-determining algorithms to smaller subproteomic collections of proteins that are already known to associate with each other in high-throughput protein-protein interaction screens, now appears to be capable of capturing a reasonably large number of low-affinity core motif sequences. Application of this approach to the genomes of yeast, fruit flies, nematodes, and humans has doubled the number of known or suspected protein-protein interaction motifs.

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