Molecular dynamics simulations of membrane proteins

Title:	Molecular dynamics simulations of membrane proteins
SNIC Project:	SNIC 2013/1-32
Project Type:	SNAC Medium
Principal Investigator:	Jens Carlsson <jens.carlsson.lab@gmail.com>
Affiliation:	Stockholm University
Duration:	2013-12-01 – 2014-12-01
Classification:	10601 10602 10407
Homepage:	http://www.carlssonlab.org/
Keywords:

Abstract

This project is focused on computational studies of membrane proteins and their interactions with small molecules. We will study the activation process of G protein-coupled receptors (GPCRs) using molecular dynamics (MD) simulations. We will MD simulations to study the activation mechanism of GPCRs. We will also use MD simulations to generate conformational ensembles for proteins that can be used in molecular docking calculations. This will enable us to take into account binding site flexibility in docking, which is on of the key problems in the field. We will also carry our large-scale molecular docking screens. In these calculations, we screen up to 5 million molecules against a receptor binding site. In this case, the focus is to identify new ligands to pharmaceutically relevant proteins.