Fragment based protein structure prediction. (c2013)
In recent years, the protein structure prediction problem has come under extensive investigation, and computational structure prediction methods are circumventing the time-consuming experimental methods by accelerating the prediction process. This work presents a fragment based protein tertiary stru...
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| Format: | masterThesis |
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2016
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| Online Access: | http://hdl.handle.net/10725/3265 https://doi.org/10.26756/th.2013.48 |
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| _version_ | 1864513460932444160 |
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| author | Terzian, Meghrig Ohanes |
| author_facet | Terzian, Meghrig Ohanes |
| author_role | author |
| dc.creator.none.fl_str_mv | Terzian, Meghrig Ohanes |
| dc.date.none.fl_str_mv | 2016-03-04T09:29:35Z 2016-03-04T09:29:35Z 2016-03-04 7/18/2013 |
| dc.identifier.none.fl_str_mv | http://hdl.handle.net/10725/3265 https://doi.org/10.26756/th.2013.48 |
| 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 Dissertations, Academic Lebanese American University -- Dissertations |
| dc.title.none.fl_str_mv | Fragment based protein structure prediction. (c2013) |
| dc.type.none.fl_str_mv | Thesis info:eu-repo/semantics/publishedVersion info:eu-repo/semantics/masterThesis |
| description | In recent years, the protein structure prediction problem has come under extensive investigation, and computational structure prediction methods are circumventing the time-consuming experimental methods by accelerating the prediction process. This work presents a fragment based protein tertiary structure prediction method that provides suboptimal structures. In addition, it demonstrates the advantage of using the CHARMM36 energy model. The method is based on a two-phase Scatter Search metaheuristic that minimizes the energy function. Backbone fragments selections extracted from the Robetta server are followed by side chain selections, extracted from the Dunbrack Library. The results, evaluated on three proteins, show that the algorithm produces tertiary structures with promising root mean square deviations, within reasonable times. |
| eu_rights_str_mv | openAccess |
| format | masterThesis |
| id | LAURepo_f13b0dd09a4c04cc77e11c367131eb33 |
| language_invalid_str_mv | en |
| network_acronym_str | LAURepo |
| network_name_str | Lebanese American University repository |
| oai_identifier_str | oai:laur.lau.edu.lb:10725/3265 |
| publishDate | 2016 |
| publisher.none.fl_str_mv | Lebanese American University |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| spelling | Fragment based protein structure prediction. (c2013)Terzian, Meghrig OhanesProteins -- Structure -- Mathematical modelsDissertations, AcademicLebanese American University -- DissertationsIn recent years, the protein structure prediction problem has come under extensive investigation, and computational structure prediction methods are circumventing the time-consuming experimental methods by accelerating the prediction process. This work presents a fragment based protein tertiary structure prediction method that provides suboptimal structures. In addition, it demonstrates the advantage of using the CHARMM36 energy model. The method is based on a two-phase Scatter Search metaheuristic that minimizes the energy function. Backbone fragments selections extracted from the Robetta server are followed by side chain selections, extracted from the Dunbrack Library. The results, evaluated on three proteins, show that the algorithm produces tertiary structures with promising root mean square deviations, within reasonable times.N/A1 hard copy: xiii, 63 leaves.; ill.; 30 cm. available at RNL.Includes bibliographical references (leaves 59-63).Lebanese American University2016-03-04T09:29:35Z2016-03-04T09:29:35Z7/18/20132016-03-04Thesisinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesishttp://hdl.handle.net/10725/3265https://doi.org/10.26756/th.2013.48eninfo:eu-repo/semantics/openAccessoai:laur.lau.edu.lb:10725/32652020-11-20T08:43:23Z |
| spellingShingle | Fragment based protein structure prediction. (c2013) Terzian, Meghrig Ohanes Proteins -- Structure -- Mathematical models Dissertations, Academic Lebanese American University -- Dissertations |
| status_str | publishedVersion |
| title | Fragment based protein structure prediction. (c2013) |
| title_full | Fragment based protein structure prediction. (c2013) |
| title_fullStr | Fragment based protein structure prediction. (c2013) |
| title_full_unstemmed | Fragment based protein structure prediction. (c2013) |
| title_short | Fragment based protein structure prediction. (c2013) |
| title_sort | Fragment based protein structure prediction. (c2013) |
| topic | Proteins -- Structure -- Mathematical models Dissertations, Academic Lebanese American University -- Dissertations |
| url | http://hdl.handle.net/10725/3265 https://doi.org/10.26756/th.2013.48 |