Chapter title |
Exploring GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method
|
---|---|
Chapter number | 8 |
Book title |
Computational Methods for GPCR Drug Discovery
|
Published in |
Methods in molecular biology, January 2018
|
DOI | 10.1007/978-1-4939-7465-8_8 |
Pubmed ID | |
Book ISBNs |
978-1-4939-7464-1, 978-1-4939-7465-8
|
Authors |
Ewa I. Chudyk, Laurie Sarrat, Matteo Aldeghi, Dmitri G. Fedorov, Mike J. Bodkin, Tim James, Michelle Southey, Roger Robinson, Inaki Morao, Alexander Heifetz |
Abstract |
The understanding of binding interactions between any protein and a small molecule plays a key role in the rationalization of affinity and selectivity. It is essential for an efficient structure-based drug design (SBDD) process. FMO enables ab initio approaches to be applied to systems that conventional quantum-mechanical (QM) methods would find challenging. The key advantage of the Fragment Molecular Orbital Method (FMO) is that it can reveal atomistic details about the individual contributions and chemical nature of each residue and water molecule toward ligand binding which would otherwise be difficult to detect without using QM methods. In this chapter, we demonstrate the typical use of FMO to analyze 19 crystal structures of β1 and β2 adrenergic receptors with their corresponding agonists and antagonists. |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 18 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 8 | 44% |
Student > Doctoral Student | 2 | 11% |
Student > Master | 2 | 11% |
Student > Ph. D. Student | 1 | 6% |
Other | 1 | 6% |
Other | 2 | 11% |
Unknown | 2 | 11% |
Readers by discipline | Count | As % |
---|---|---|
Chemistry | 6 | 33% |
Biochemistry, Genetics and Molecular Biology | 3 | 17% |
Agricultural and Biological Sciences | 2 | 11% |
Chemical Engineering | 1 | 6% |
Pharmacology, Toxicology and Pharmaceutical Science | 1 | 6% |
Other | 2 | 11% |
Unknown | 3 | 17% |