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Protein Structure Refinement Algorithms


Chitsaz, Mohsen (2014) Protein Structure Refinement Algorithms. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/7731-QM74.


Protein structure prediction has remained a major challenge in structural biology for more than half a century. Accelerated and cost efficient sequencing technologies have allowed researchers to sequence new organisms and discover new protein sequences. Novel protein structure prediction technologies will allow researchers to study the structure of proteins and to determine their roles in the underlying biology processes and develop novel therapeutics.

Difficulty of the problem stems from two folds: (a) describing the energy landscape that corresponds to the protein structure, commonly referred to as force field problem; and (b) sampling of the energy landscape, trying to find the lowest energy configuration that is hypothesized to be the native state of the structure in solution. The two problems are interweaved and they have to be solved simultaneously. This thesis is composed of three major contributions. In the first chapter we describe a novel high-resolution protein structure refinement algorithm called GRID. In the second chapter we present REMCGRID, an algorithm for generation of low energy decoy sets. In the third chapter, we present a machine learning approach to ranking decoys by incorporating coarse-grain features of protein structures.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Protein Folding, Protein Structure Determination, Stochastic Sampling, High-resolution refinement
Degree Grantor:California Institute of Technology
Division:Biology and Biological Engineering
Major Option:Biochemistry and Molecular Biophysics
Minor Option:Computer Science
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Mayo, Stephen L.
Thesis Committee:
  • Goddard, William A., III (chair)
  • Bjorkman, Pamela Jane (co-chair)
  • Umans, Christopher M.
  • Mayo, Stephen L.
Defense Date:14 March 2014
Non-Caltech Author Email:mhchitsaz (AT)
Additional Information:This thesis aims at investigating protein structure refinement algorithms and proteins structure prediction
Funding AgencyGrant Number
Defense Advanced Research Projects AgencyUNSPECIFIED
Record Number:CaltechTHESIS:06072014-074257676
Persistent URL:
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:8502
Deposited By: Mohsen Chitsaz
Deposited On:10 Jun 2014 21:09
Last Modified:04 Oct 2019 00:05

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