{"id":{"repo_id":"wku-diss","oai_identifier":"oai:digitalcommons.wku.edu:theses-1104"},"canonical_url":"https://search.dev.ndltd.org/etd/wku-diss/oai:digitalcommons.wku.edu:theses-1104","repository":{"repo_id":"wku-diss","name":"Western Kentucky University","base_url":"https://digitalcommons.wku.edu/do/oai/"},"display":{"title":"Geometric Build-up Solutions for Protein Determination via Distance Geometry","abstract":"Proteins carry out an almost innumerable amount of biological processes that are absolutely necessary to life and as a result proteins and their structures are very often the objects of study in research. As such, this thesis will begin with a description of protein function and structure, followed by brief discussions of the two major experimental structure determination methods. Another problem that often arises in molecular modeling is referred to as the Molecular Distance Geometry Problem (MDGP). This problem seeks to find coordinates for the atoms of a protein or molecule when given only a set of pair-wise distances between atoms. To introduce the complexities of the MDGP we begin at its origins in distance geometry and progress to the specific sub-problems and some of the solutions that have been developed. This is all in preparation for a discussion of what is known as the Geometric Build-up (GBU) Solution. This solution has lead to the development of several algorithms and continues to be modified to account for more and different complexities. The culmination of this thesis, then, is a new algorithm, the Revised Updated Geometric Build-up, that is faster than previous GBU’s while maintaining the accuracy of the resulting structure.","abstract_html":"Proteins carry out an almost innumerable amount of biological processes that are absolutely necessary to life and as a result proteins and their structures are very often the objects of study in research. As such, this thesis will begin with a description of protein function and structure, followed by brief discussions of the two major experimental structure determination methods. Another problem that often arises in molecular modeling is referred to as the Molecular Distance Geometry Problem (MDGP). This problem seeks to find coordinates for the atoms of a protein or molecule when given only a set of pair-wise distances between atoms. To introduce the complexities of the MDGP we begin at its origins in distance geometry and progress to the specific sub-problems and some of the solutions that have been developed. This is all in preparation for a discussion of what is known as the Geometric Build-up (GBU) Solution. This solution has lead to the development of several algorithms and continues to be modified to account for more and different complexities. The culmination of this thesis, then, is a new algorithm, the Revised Updated Geometric Build-up, that is faster than previous GBU’s while maintaining the accuracy of the resulting structure.","abstract_has_math":false,"creators":["Davis, Robert Tucker"],"institution":null,"degree_name":"Master of Science in Applied Mathematics","degree_level":null,"degree_discipline":"Department of Mathematics and Computer Science","degree_department":null,"school":null,"contributors":["Dr. Di Wu (Director), Dr. Claus Ernst, Dr. Claire A. Rinehart"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2009,"date_issued":"2009-08-01T07:00:00Z","date_published":"2009-08-01T07:00:00Z","updated_at":"2026-07-24T06:07:03Z","subjects":["Molecular Distance Geometry Problem (MDGP)","Geometric Build-up (GBU) Solution","mathematical modeling of protein structure","Applied Mathematics","Biochemistry","Molecular Biology","Structural Biology"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://digitalcommons.wku.edu/theses/102","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Dr. Di Wu (Director), Dr. Claus Ernst, Dr. Claire A. 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As such, this thesis will begin with a description of protein function and structure, followed by brief discussions of the two major experimental structure determination methods. Another problem that often arises in molecular modeling is referred to as the Molecular Distance Geometry Problem (MDGP). This problem seeks to find coordinates for the atoms of a protein or molecule when given only a set of pair-wise distances between atoms. To introduce the complexities of the MDGP we begin at its origins in distance geometry and progress to the specific sub-problems and some of the solutions that have been developed. This is all in preparation for a discussion of what is known as the Geometric Build-up (GBU) Solution. This solution has lead to the development of several algorithms and continues to be modified to account for more and different complexities. The culmination of this thesis, then, is a new algorithm, the Revised Updated Geometric Build-up, that is faster than previous GBU’s while maintaining the accuracy of the resulting structure."]},{"key":"dc:title","label":"Title","values":["Geometric Build-up Solutions for Protein Determination via Distance Geometry"]}]}],"canonical_facts":{"dc:contributor":["Dr. Di Wu (Director), Dr. Claus Ernst, Dr. Claire A. Rinehart"],"dc:creator":["Davis, Robert Tucker"],"dc:description.abstract":["Proteins carry out an almost innumerable amount of biological processes that are absolutely necessary to life and as a result proteins and their structures are very often the objects of study in research. As such, this thesis will begin with a description of protein function and structure, followed by brief discussions of the two major experimental structure determination methods. Another problem that often arises in molecular modeling is referred to as the Molecular Distance Geometry Problem (MDGP). This problem seeks to find coordinates for the atoms of a protein or molecule when given only a set of pair-wise distances between atoms. To introduce the complexities of the MDGP we begin at its origins in distance geometry and progress to the specific sub-problems and some of the solutions that have been developed. This is all in preparation for a discussion of what is known as the Geometric Build-up (GBU) Solution. This solution has lead to the development of several algorithms and continues to be modified to account for more and different complexities. The culmination of this thesis, then, is a new algorithm, the Revised Updated Geometric Build-up, that is faster than previous GBU’s while maintaining the accuracy of the resulting structure."],"dc:identifier":["https://digitalcommons.wku.edu/theses/102"],"dc:subject":["Molecular Distance Geometry Problem (MDGP)","Geometric Build-up (GBU) Solution","mathematical modeling of protein structure","Applied Mathematics","Biochemistry","Molecular Biology","Structural Biology"],"dc:title":["Geometric Build-up Solutions for Protein Determination via Distance Geometry"],"dc:type":["Thesis"],"thesis:degree_discipline":["Department of Mathematics and Computer Science"],"thesis:degree_name":["Master of Science in Applied Mathematics"]},"updated_at":"2026-07-24T06:07:03Z"}