Biology Ph.D. Dissertations


Building Representative Sets Of RNA 3D Structures and Selecting High Quality Loops

Date of Award


Document Type


Degree Name

Doctor of Philosophy (Ph.D.)


Biological Sciences

First Advisor

Neocles Leontis (Advisor)

Second Advisor

Raymond Larsen (Committee Member)

Third Advisor

George Bullerjahn (Committee Member)

Fourth Advisor

Hans Wildschutte (Committee Member)

Fifth Advisor

Howard Cromwell (Other)


This dissertation contains two types of work. The first is the creation and maintenance of our data pipeline. This chapter focuses on the technical work behind the extension of our pipeline. In general, this work extends our previous pipeline to import more data as well as standardizing several parts of the pipeline. As a result, this work provides a framework for future modifications of the pipeline. This work was driven both by the move from RNA 3D structures being provided in mmCIF format instead of the more limited PDB format, as well as the need to clean up the previous version of the pipeline.

The second type of work is scientific including my work on creating equivalence classes for all RNA 3D structures, using these sets to build representative sets and then how to use these representative sets along with new quality data to select a set of high quality loops for future analysis. The new work on equivalence classes and representative sets was driven by the move from PDB to mmCIF formats. This move forced the redesign of the previous method, as it would only use the largest chain in each PDB file. This change allowed me to reconsider the approach and allowed several improvements.

The work on loop quality was prompted by the release of new structure quality data, Real Space R Z-Score (RSRZ). This data allows the examination of how well a proposed structure fits the data it is built from. By using this we can limit our studies of RNA loops to only those that are from high quality, well modeled structures.