Computational investigation of high affinity ligand binding to proteins

Summary

Design of high-affinity ligands for protein targets using docking, molecular dynamics simulations and quantitative structure-activity relations.

Supervisor(s)

Associate Professor Serdar Kuyucak

Research Location

School of Physics

Program Type

Masters/PHD

Synopsis

Proteins are primary targets for development of therapeutic drugs for many diseases. Finding a compound that binds selectively to a target protein with high affinity is usually a long and expensive task in the laboratory. Complementing laboratory work with computational methods will help to rationalize this task and speed up the ligand-screening process. The aim of this project is to develop simulation tools for fast and accurate screening of ligands and use these methods to find compounds that bind strongly to a target protein. For this purpose docking, molecular dynamics simulations and quantitative structure-activity relations will be used in combination. The knowledge gathered from the analysis of quantitative structure-activity relations will be harnessed in design of new compounds that have higher affinity than currently known drugs.

Additional Information

HDR Inherent Requirements

In addition to the academic requirements set out in the Science Postgraduate Handbook, you may be required to satisfy a number of inherent requirements to complete this degree. Example of inherent requirement may include:

- Confidential disclosure and registration of a disability that may hinder your performance in your degree;
- Confidential disclosure of a pre-existing or current medical condition that may hinder your performance in your degree (e.g. heart disease, pace-maker, significant immune suppression, diabetes, vertigo, etc.);
- Ability to perform independently and/or with minimal supervision;
- Ability to undertake certain physical tasks (e.g. heavy lifting);
- Ability to undertake observatory, sensory and communication tasks;
- Ability to spend time at remote sites (e.g. One Tree Island, Narrabri and Camden);
- Ability to work in confined spaces or at heights;
- Ability to operate heavy machinery (e.g. farming equipment);
- Hold or acquire an Australian driver’s licence;
- Hold a current scuba diving license;
- Hold a current Working with Children Check;
- Meet initial and ongoing immunisation requirements (e.g. Q-Fever, Vaccinia virus, Hepatitis, etc.)

You must consult with your nominated supervisor regarding any identified inherent requirements before completing your application.

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Keywords

physics, Biophysics, computational biology, molecular dynamics, protein-ligand interactions, rational drug design

Opportunity ID

The opportunity ID for this research opportunity is: 908

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