| Chapter title |
Protein-Peptide Interaction Design: PepCrawler and PinaColada
|
|---|---|
| Chapter number | 16 |
| Book title |
Modeling Peptide-Protein Interactions
|
| Published in |
Methods in molecular biology, February 2017
|
| DOI | 10.1007/978-1-4939-6798-8_16 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-6796-4, 978-1-4939-6798-8
|
| Authors |
Daniel Zaidman, Haim J. Wolfson |
| Editors |
Ora Schueler-Furman, Nir London |
| 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. |
Mendeley readers
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 11 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Other | 2 | 18% |
| Researcher | 2 | 18% |
| Student > Doctoral Student | 1 | 9% |
| Student > Bachelor | 1 | 9% |
| Student > Ph. D. Student | 1 | 9% |
| Other | 3 | 27% |
| Unknown | 1 | 9% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 5 | 45% |
| Computer Science | 2 | 18% |
| Agricultural and Biological Sciences | 2 | 18% |
| Psychology | 1 | 9% |
| Unknown | 1 | 9% |