Chapter title |
Identifying Loop-Mediated Protein–Protein Interactions Using LoopFinder
|
---|---|
Chapter number | 15 |
Book title |
Modeling Peptide-Protein Interactions
|
Published in |
Methods in molecular biology, February 2017
|
DOI | 10.1007/978-1-4939-6798-8_15 |
Pubmed ID | |
Book ISBNs |
978-1-4939-6796-4, 978-1-4939-6798-8
|
Authors |
Timothy R. Siegert, Michael Bird, Joshua A. Kritzer |
Editors |
Ora Schueler-Furman, Nir London |
Abstract |
Peptides are an increasingly useful class of molecules, finding unique applications as chemical probes and potential drugs. They are particularly adept at inhibiting protein-protein interactions, which are often difficult to target using small molecules. The identification and rational design of protein-binding epitopes remains a bottleneck in the development of bioactive peptides. One fruitful strategy has been using structured scaffolds to present essential hot spot residues involved in protein-protein recognition, and this process has been greatly advanced by computational tools that can identify hot spot residues. Here we discuss LoopFinder, a program that uses structures from the Protein Data Bank to comprehensively search for protein-protein interactions that are mediated by nonhelical, nonsheet loop structures. We developed LoopFinder to identify these "hot loops" and to assist in the design of cyclic peptides that mimic these important structures. In this article, we provide all key files, outline step-by-step methods for users to conduct independent LoopFinder searches, and provide guidance on additional potential applications for the LoopFinder program. |
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Country | Count | As % |
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Unknown | 10 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
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Other | 2 | 20% |
Student > Ph. D. Student | 2 | 20% |
Professor | 1 | 10% |
Professor > Associate Professor | 1 | 10% |
Student > Postgraduate | 1 | 10% |
Other | 0 | 0% |
Unknown | 3 | 30% |
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Linguistics | 1 | 10% |
Unknown | 3 | 30% |