Scatter search metaheuristic for homology based protein structure prediction. (c2015)
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...
محفوظ في:
| المؤلف الرئيسي: | |
|---|---|
| التنسيق: | masterThesis |
| منشور في: |
2015
|
| الموضوعات: | |
| الوصول للمادة أونلاين: | http://hdl.handle.net/10725/2215 https://doi.org/10.26756/th.2015.20 |
| الوسوم: |
إضافة وسم
لا توجد وسوم, كن أول من يضع وسما على هذه التسجيلة!
|
| _version_ | 1864513457522475008 |
|---|---|
| author | Stamboulian, Mouses Hrag |
| author_facet | Stamboulian, Mouses Hrag |
| author_role | author |
| dc.creator.none.fl_str_mv | Stamboulian, Mouses Hrag |
| dc.date.none.fl_str_mv | 2015-09-30T08:50:01Z 2015-09-30T08:50:01Z 2015 2015-09-30 2015-05-21 |
| dc.identifier.none.fl_str_mv | http://hdl.handle.net/10725/2215 https://doi.org/10.26756/th.2015.20 |
| dc.language.none.fl_str_mv | en |
| dc.publisher.none.fl_str_mv | Lebanese American University |
| dc.rights.*.fl_str_mv | info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Proteins -- Structure -- Mathematical models Sequence alignment (Bioinformatics) Scattering (Mathematics) Lebanese American University -- Dissertations Dissertations, Academic |
| dc.title.none.fl_str_mv | Scatter search metaheuristic for homology based protein structure prediction. (c2015) |
| dc.type.none.fl_str_mv | Thesis info:eu-repo/semantics/publishedVersion info:eu-repo/semantics/masterThesis |
| description | 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. |
| eu_rights_str_mv | openAccess |
| format | masterThesis |
| id | LAURepo_b3d7439d7b09f9d883b27fe0cd484a4b |
| language_invalid_str_mv | en |
| network_acronym_str | LAURepo |
| network_name_str | Lebanese American University repository |
| oai_identifier_str | oai:laur.lau.edu.lb:10725/2215 |
| publishDate | 2015 |
| publisher.none.fl_str_mv | Lebanese American University |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| spelling | Scatter search metaheuristic for homology based protein structure prediction. (c2015)Stamboulian, Mouses HragProteins -- Structure -- Mathematical modelsSequence alignment (Bioinformatics)Scattering (Mathematics)Lebanese American University -- DissertationsDissertations, AcademicDetermining 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.N/A1 hard copy: xiii, 74 leave; ill. (some col.); 30 cm. available at RNL.Includes bibliographical references (leaves 63-71).Lebanese American University2015-09-30T08:50:01Z2015-09-30T08:50:01Z20152015-09-302015-05-21Thesisinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesishttp://hdl.handle.net/10725/2215https://doi.org/10.26756/th.2015.20eninfo:eu-repo/semantics/openAccessoai:laur.lau.edu.lb:10725/22152020-11-20T08:43:23Z |
| spellingShingle | Scatter search metaheuristic for homology based protein structure prediction. (c2015) Stamboulian, Mouses Hrag Proteins -- Structure -- Mathematical models Sequence alignment (Bioinformatics) Scattering (Mathematics) Lebanese American University -- Dissertations Dissertations, Academic |
| status_str | publishedVersion |
| title | Scatter search metaheuristic for homology based protein structure prediction. (c2015) |
| title_full | Scatter search metaheuristic for homology based protein structure prediction. (c2015) |
| title_fullStr | Scatter search metaheuristic for homology based protein structure prediction. (c2015) |
| title_full_unstemmed | Scatter search metaheuristic for homology based protein structure prediction. (c2015) |
| title_short | Scatter search metaheuristic for homology based protein structure prediction. (c2015) |
| title_sort | Scatter search metaheuristic for homology based protein structure prediction. (c2015) |
| topic | Proteins -- Structure -- Mathematical models Sequence alignment (Bioinformatics) Scattering (Mathematics) Lebanese American University -- Dissertations Dissertations, Academic |
| url | http://hdl.handle.net/10725/2215 https://doi.org/10.26756/th.2015.20 |