Modeling of protein-ligand binding
Title: |
Modeling of protein-ligand binding |
DNr: |
SNIC 2019/32-14 |
Project Type: |
SNIC Small Storage |
Principal Investigator: |
Yaoquan Tu <yaoquan@kth.se> |
Affiliation: |
Kungliga Tekniska högskolan |
Duration: |
2019-12-01 – 2020-12-01 |
Classification: |
10407 |
Homepage: |
https://www.kth.se/profile/yaoquan |
Keywords: |
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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 metadynamics, 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.