| Chapter title |
A Practical Introduction to Molecular Dynamics Simulations: Applications to Homology Modeling
|
|---|---|
| Chapter number | 6 |
| Book title |
Homology Modeling
|
| Published in |
Methods in molecular biology, January 2012
|
| DOI | 10.1007/978-1-61779-588-6_6 |
| Pubmed ID | |
| Book ISBNs |
978-1-61779-587-9, 978-1-61779-588-6
|
| Authors |
Alessandra Nurisso, Antoine Daina, Ross C. Walker, Nurisso, Alessandra, Daina, Antoine, Walker, Ross C. |
| Abstract |
In this chapter, practical concepts and guidelines are provided for the use of molecular dynamics (MD) simulation for the refinement of homology models. First, an overview of the history and a theoretical background of MD are given. Literature examples of successful MD refinement of homology models are reviewed before selecting the Cytochrome P450 2J2 structure as a case study. We describe the setup of a system for classical MD simulation in a detailed stepwise fashion and how to perform the refinement described in the publication of Li et al. (Proteins 71:938-949, 2008). This tutorial is based on version 11 of the AMBER Molecular Dynamics software package (http://ambermd.org/). However, the approach discussed is equally applicable to any condensed phase MD simulation environment. |
Mendeley readers
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Russia | 1 | 2% |
| Unknown | 52 | 98% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 11 | 21% |
| Student > Bachelor | 9 | 17% |
| Researcher | 8 | 15% |
| Student > Master | 5 | 9% |
| Professor | 4 | 8% |
| Other | 7 | 13% |
| Unknown | 9 | 17% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 13 | 25% |
| Agricultural and Biological Sciences | 13 | 25% |
| Pharmacology, Toxicology and Pharmaceutical Science | 3 | 6% |
| Chemistry | 3 | 6% |
| Medicine and Dentistry | 3 | 6% |
| Other | 9 | 17% |
| Unknown | 9 | 17% |