Title:	Modeling of protein-ligand binding
DNr:	SNIC 2015/1-396
Project Type:	SNIC Medium Compute
Principal Investigator:	Yaoquan Tu <yaoquan@kth.se>
Affiliation:	Kungliga Tekniska högskolan
Duration:	2015-11-01 – 2016-11-01
Classification:	10402 10603 30101
Homepage:	http://www.theochem.kth.se/people/tu/
Keywords:

Abstract

A ligand binding to a protein can change the structure and functions of the protein and therefore affect the related biological processes. Protein-ligand binding occurs in many biological processes. The knowledge of protein-ligand binding is also essential in structure-based drug design. Although the structures of ligand-binding domains of many important proteins have been determined experimentally, our understanding of protein-ligand interactions is still limited. For example, the ligand-binding affinity, which is a measure of the strength of the protein-ligand interactions, is still hard to determine both experimentally and theoretically. In this project, we will use new modeling approaches, such as steered molecular dynamics simulations, to the study of ligand-protein interactions, including ligand binding modes and binding affinities. As water molecules in the protein receptors play crucial roles in ligand-protein interactions, the roles of water molecules in ligand-protein interactions and in the design of new ligand molecules will also be studied. By applying new modeling methods to the studies of protein-ligand interaction, we aim to elucidate the mechanism of protein-ligand interactions at the atomistic level.