Scatter search metaheuristic for homology based protein structure prediction. (c2015)

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dc.contributor.author Stamboulian, Mouses Hrag
dc.date.accessioned 2015-09-30T08:50:01Z
dc.date.available 2015-09-30T08:50:01Z
dc.date.copyright 2015 en_US
dc.date.issued 2015-09-30
dc.date.submitted 2015-05-21
dc.identifier.uri http://hdl.handle.net/10725/2215
dc.description.abstract Determining a protein’s structure is a challenging goal in structural bioinformatics, offering important insight towards understanding the function of a protein. Homology modeling is an effective technique in protein structure prediction (PSP). However this technique suffers from poor initial target-template alignments, especially when the sequence identity between the two falls below 25%. To improve homology based PSP, we propose a scatter search (SS) metaheuristic algorithm. Our algorithm optimizes the initial poor alignments, generated by a dynamic programming method. 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. The metaheuristic is guided using two fitness functions, GA341 and DOPE. 3D models are generated using the software MODELLER. We assess our algorithm on a total of 11 proteins whose structures are present in the Protein Data Bank (PDB) and which has been used in previous literature. Results obtained by our algorithm are compared with other homology modeling approaches as well as a pure ab-initio and a fragment based assembly approach. The 3D models predicted by our algorithm show improved root mean standard deviations (RMSD) with respect to the native structures. en_US
dc.language.iso en en_US
dc.subject Proteins -- Structure -- Mathematical models en_US
dc.subject Sequence alignment (Bioinformatics) en_US
dc.subject Scattering (Mathematics) en_US
dc.subject Lebanese American University -- Dissertations en_US
dc.subject Dissertations, Academic en_US
dc.title Scatter search metaheuristic for homology based protein structure prediction. (c2015) en_US
dc.type Thesis en_US
dc.term.submitted Spring en_US
dc.author.degree MS in Computer Science en_US
dc.author.school SAS en_US
dc.author.idnumber 201206167 en_US
dc.author.commembers Haraty, Ramzi
dc.author.commembers Tokajian, Sima
dc.author.woa OA en_US
dc.author.department Computer Science en_US
dc.description.embargo N/A en_US
dc.description.physdesc 1 hard copy: xiii, 74 leave; ill. (some col.); 30 cm. available at RNL. en_US
dc.author.advisor Mansour, Nashat
dc.keywords Comparative Modeling en_US
dc.keywords Homology Modeling en_US
dc.keywords Protein Structure Prediction en_US
dc.keywords Scatter Search en_US
dc.keywords Metaheuristics en_US
dc.description.bibliographiccitations Includes bibliographical references (leaves 63-71). en_US
dc.identifier.doi https://doi.org/10.26756/th.2015.20 en_US
dc.publisher.institution Lebanese American University en_US

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