title: Protein-Peptide Interaction Design: PepCrawler and PinaColada.
abstract: In this chapter we present two methods related to rational design of inhibitory peptides: PepCrawler: A tool to derive binding peptides from protein-protein complexes and the prediction of protein-peptide complexes. Given an initial protein-peptide complex, the method detects improved predicted peptide binding conformations which bind the protein with higher affinity. This program is a robotics motivated algorithm, representing the peptide as a robotic arm moving among obstacles and exploring its conformational space in an efficient way. PinaColada: A peptide design program for the discovery of novel peptide candidates that inhibit protein-protein interactions. PinaColada uses PepCrawler while introducing sequence mutations, in order to find novel inhibitory peptides for PPIs. It uses the ant colony optimization approach to explore the peptide's sequence space, while using PepCrawler in the refinement stage.
authors.affiliation: Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, 69978, Israel.
authors.forename: Daniel
authors.initials: D
authors.lastname: Zaidman
authors.affiliation: Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, 69978, Israel. wolfson@tau.ac.il.
authors.forename: Haim J
authors.initials: HJ
authors.lastname: Wolfson
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D015195:Drug Design; D006801:Humans; D008958:Models, Molecular; D010446:Peptide Fragments / Q000737:chemistry / Q000494:pharmacology*; D011485:Protein Binding; D011487:Protein Conformation; D060066:Protein Interaction Maps / Q000187:drug effects*; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*
chemical_list: D010446:Peptide Fragments; D011506:Proteins
keywords: Ant colony optimization; Computer aided drug design; Inhibitor design; Peptides; Protein–protein interaction inhibitors; RRT