Chapter title |
Highly Flexible Protein-Peptide Docking Using CABS-Dock
|
---|---|
Chapter number | 6 |
Book title |
Modeling Peptide-Protein Interactions
|
Published in |
Methods in molecular biology, February 2017
|
DOI | 10.1007/978-1-4939-6798-8_6 |
Pubmed ID | |
Book ISBNs |
978-1-4939-6796-4, 978-1-4939-6798-8
|
Authors |
Maciej Pawel Ciemny, Mateusz Kurcinski, Konrad Jakub Kozak, Andrzej Kolinski, Sebastian Kmiecik, Maciej Paweł Ciemny |
Editors |
Ora Schueler-Furman, Nir London |
Abstract |
Protein-peptide molecular docking is a difficult modeling problem. It is even more challenging when significant conformational changes that may occur during the binding process need to be predicted. In this chapter, we demonstrate the capabilities and features of the CABS-dock server for flexible protein-peptide docking. CABS-dock allows highly efficient modeling of full peptide flexibility and significant flexibility of a protein receptor. During CABS-dock docking, the peptide folding and binding process is explicitly simulated and no information about the peptide binding site or its structure is used. This chapter presents a successful CABS-dock use for docking a potentially therapeutic peptide to a protein target. Moreover, simulation contact maps, a new CABS-dock feature, are described and applied to the docking test case. Finally, a tutorial for running CABS-dock from the command line or command line scripts is provided. The CABS-dock web server is available from http://biocomp.chem.uw.edu.pl/CABSdock/ . |
X Demographics
Geographical breakdown
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Norway | 1 | 33% |
Unknown | 2 | 67% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 3 | 100% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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Unknown | 42 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
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Student > Ph. D. Student | 7 | 17% |
Researcher | 6 | 14% |
Other | 4 | 10% |
Student > Master | 4 | 10% |
Student > Bachelor | 3 | 7% |
Other | 6 | 14% |
Unknown | 12 | 29% |
Readers by discipline | Count | As % |
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Biochemistry, Genetics and Molecular Biology | 10 | 24% |
Agricultural and Biological Sciences | 7 | 17% |
Chemistry | 4 | 10% |
Chemical Engineering | 3 | 7% |
Computer Science | 2 | 5% |
Other | 3 | 7% |
Unknown | 13 | 31% |