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A global optimization approach for searching low energy conformations of proteins

Roy, Shantanu. A global optimization approach for searching low energy conformations of proteins. 2010, PhD Thesis, University of Basel, Faculty of Science.

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Official URL: http://edoc.unibas.ch/diss/DissB_9226

Abstract

De novo protein structure prediction and understanding the protein folding mechanism is an outstanding challenge of Biological Physics. Relying on the thermodynamic hypothesis of protein folding it is expected that the native state of a protein can be found out if the global minimum of the free energy surface is found. To understand the energy landscape or the free energy surface is challenging. The structure and dynamics of proteins are the manifestations of the underlying potential energy surface. Here the potential energy function stands on a framework of all-atom representation and uses purely physics-based interactions. For the solvated proteins the effective free energy is defined as an implicit solvation model which includes the solvation free energy, along with a standard all-atom biomolecular forcefield. A major challenge is to search for the global minimum on this effective free energy surface. In this work the Minima Hopping Algorithm (MHOP) to find global minima on potential energy surfaces has been used for protein structure prediction or in general finding the lowest energy conformations of proteins. Here proteins have been studied both in vacuo and in the aqueous medium. For short peptides starting from a completely extended conformation we could find conformational minima which are very close to the experimentally observed structures.
Advisors:Goedecker, Stefan
Committee Members:Field, Martin J. and Schwede, Torsten
Faculties and Departments:05 Faculty of Science > Departement Physik > Physik > Physik (Goedecker)
Item Type:Thesis
Thesis no:9226
Bibsysno:Link to catalogue
Number of Pages:133 S.
Language:English
Identification Number:
Last Modified:30 Jun 2016 10:41
Deposited On:19 Nov 2010 09:05

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