Biology Reference
In-Depth Information
CHAPTER
GPCR Oligomerization
5
Agnieszka A. Kaczor
*
,{
, Jana Selent
{
, and Antti Poso
*
Structure-Based Molecular
Modeling Approaches to
*
Department of Pharmaceutical Chemistry, School of Pharmacy, University
of Eastern Finland, Kuopio, Finland
{
Department of Chemical Technology of Pharmaceutical Substances with Computer Modeling Lab,
Faculty of Pharmacy with Division of Medical Analytics, Medical University
of Lublin, Lublin, Poland
{
Research Unit on Biomedical Informatics (GRIB), PRBB, Barcelona, Spain
CHAPTER OUTLINE
Introduction .............................................................................................................. 92
5.1 Protein-Protein Docking..................................................................................... 93
5.1.1 Available Docking Programs .............................................................. 94
5.1.2 Practical Aspects.............................................................................. 95
5.1.3 Reliability ........................................................................................ 96
5.2 MD Simulation ................................................................................................... 96
5.2.1 Recent Milestones in Simulating GPCRs............................................. 97
5.2.2 Technical Aspects ............................................................................ 98
5.3 Normal Mode Analysis ....................................................................................... 99
5.3.1 Background and Examples of Applications.......................................... 99
5.3.2 Software ........................................................................................ 100
5.4 Electrostatics Studies....................................................................................... 100
5.4.1 Background and Examples of Application ......................................... 100
5.4.2 Software ........................................................................................ 101
Acknowledgments ................................................................................................... 101
References ............................................................................................................. 102
Abstract
Classical structure-based drug design techniques using G-protein-coupled receptors
(GPCRs) as targets focus nearly exclusively on binding at the orthosteric site of a
single receptor. Dimerization and oligomerization of GPCRs, proposed almost
