‫التقرير النهائي‬
Administrative Information
‫المعلومات االدارية‬
03-05-08
:‫المرجع‬
Project Title - )‫عنوان المشروع (عربي وأجنبي‬
‫طريقة حاسوبية الكتشاف تركيبة البروتين‬
Computational method for protein structure prediction
Principal Investigator - ‫الباحث الرئيسي‬
‫رقم الهاتف‬
‫العنوان االلكتروني‬
Telephone
e-mail
03-379647 nmansour@lau.edu.lb
‫العنوان‬
Address
Beirut
‫الوظيفية‬
Post
‫المؤسسة‬
Institution
MnreaanM nr
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‫االسم‬
Name
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Co-Workers - ‫الباحثون المشاركون‬
‫العنوان االلكتروني‬
e-mail
Hassan.khashfe@balamand.edu.lb
‫المؤسسة‬
‫االسم‬
Institution
Name
Balamand Hassan Khashfe
University
2 years
: Duration -‫المدة التعاقدية للمشروع‬
Scientific Information
‫العلمية‬
‫المعلومات‬
ّ
Objectives - ‫الهدف‬
The objective of the project was to determine the folding of proteins given their molecular
composition. This will be done by using computational methods to simulate the folding of
proteins.
Achievements -‫أالنجازات المحققة‬
1. A computational metaheuristic, based on scatter search, was designed and implemented
for the ab inito protein structure prediction (PSP).
2. This metaheuristic was tested on proteins derived from the protein data bank (PDB),
where their solutions are known. Our algorithm produced promising 3D protein
structures in terms of the standard root mean square deviation (RMSD) of the resulting
structures. The RMSD was reasonable for small proteins.
3. The challenges remain in further reducing the RMSD of the produced proteins, reducing
the execution time of the program, selecting adequate energy expression that guide the
PSP process, and extending the application of the metaheuristic to medium-size
proteins.
Perspectives - ‫آفاق البحث‬
Future work shall focus on:
1. Computationally evaluating the free energy functions used to guide the PSP solution
strategies. The objective will be to devise more adequate energy expressions.
2. Improving the design of the metaheuristic in order to produce lower RMSD values. In
particular, we need to ensure that the metaheuristic preserves the standard bond lengths
among atoms in the protein.
3. Exploring parallel methods for reducing program execution time.
Publications & Communications - ‫المنشورات والمساهمات في المؤتمرات‬
1. Mansour, N., Kehyayan, C., and Khashfe, H. (2009). Scatter Search algorithm for
Protein Structure Prediction. Int. J. Bioinformatics Research and Applications, Vol. 5,
No. 5 pp. 501-515.
2. Mansour, N., Ghalayini, I., Rizk, S., Sibai, M. (2011). Evolutionary Algorithm For
Predicting All-Atom Protein Structure .Int. Conf. On Bioinformatics And Computational
Biology, Mar. 23 - 25, New Orleans, Louisiana, USA.
Abstract - ‫موجز عن نتائج البحث‬
We have designed a Scatter Search (SS) algorithm for predicting 3D structures of proteins
based on torsion angles representation. Given the protein’s sequence of Amino Acids (AAs),
our algorithm produces a 3D structure that aims to minimize the energy function associated
with the structure. SS is an evolutionary approach that is based on a population of candidate
solutions. These candidates undergo evolutionary operations that combine search intensification
and diversification over a number of iterations. We evaluated our algorithm on three proteins
taken from a Protein Data Bank (PDB). The results show that our algorithm is able to produce
3D structures with good sub-optimal energy values. Also, the Root Mean Square Deviations
(RMSD) of these structures from the reference proteins are promising within limits imposed by
the assumptions made.