Chapter title |
Protein–Protein Docking in Drug Design and Discovery
|
---|---|
Chapter number | 15 |
Book title |
Computational Drug Discovery and Design
|
Published in |
Methods in molecular biology, January 2018
|
DOI | 10.1007/978-1-4939-7756-7_15 |
Pubmed ID | |
Book ISBNs |
978-1-4939-7755-0, 978-1-4939-7756-7
|
Authors |
Agnieszka A. Kaczor, Damian Bartuzi, Tomasz Maciej Stępniewski, Dariusz Matosiuk, Jana Selent |
Abstract |
Protein-protein interactions (PPIs) are responsible for a number of key physiological processes in the living cells and underlie the pathomechanism of many diseases. Nowadays, along with the concept of so-called "hot spots" in protein-protein interactions, which are well-defined interface regions responsible for most of the binding energy, these interfaces can be targeted with modulators. In order to apply structure-based design techniques to design PPIs modulators, a three-dimensional structure of protein complex has to be available. In this context in silico approaches, in particular protein-protein docking, are a valuable complement to experimental methods for elucidating 3D structure of protein complexes. Protein-protein docking is easy to use and does not require significant computer resources and time (in contrast to molecular dynamics) and it results in 3D structure of a protein complex (in contrast to sequence-based methods of predicting binding interfaces). However, protein-protein docking cannot address all the aspects of protein dynamics, in particular the global conformational changes during protein complex formation. In spite of this fact, protein-protein docking is widely used to model complexes of water-soluble proteins and less commonly to predict structures of transmembrane protein assemblies, including dimers and oligomers of G protein-coupled receptors (GPCRs). In this chapter we review the principles of protein-protein docking, available algorithms and software and discuss the recent examples, benefits, and drawbacks of protein-protein docking application to water-soluble proteins, membrane anchoring and transmembrane proteins, including GPCRs. |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 44 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Master | 9 | 20% |
Researcher | 7 | 16% |
Student > Ph. D. Student | 4 | 9% |
Student > Bachelor | 3 | 7% |
Professor | 2 | 5% |
Other | 5 | 11% |
Unknown | 14 | 32% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 15 | 34% |
Chemistry | 6 | 14% |
Pharmacology, Toxicology and Pharmaceutical Science | 2 | 5% |
Unspecified | 1 | 2% |
Psychology | 1 | 2% |
Other | 3 | 7% |
Unknown | 16 | 36% |