Publications/Theses

Christian Schudoma

Contact author at chris-at-darkjade-net

M.Sc. Thesis: A Fragment Based Approach to RNA Threading

ABSTRACT:

The analysis of the relations between structure and function of a
biopolymer such as RNA is a core issue in structural biology and
bioinformatics. The folding process of RNA structure follows a strict
hierarchical scheme. The native structure of an RNA molecule is formed
by the subsequent formation of secondary and tertiary structure
motifs. These motifs are common in RNA molecules of different species,
suggesting that parts (fragments) of a molecule with known structure
can be used to predict unknown RNA structures. This thesis describes
methods for an approach on the modeling of RNA three-dimensional
structure based on structure fragments. We describe the design and
composition of a novel template fragment library, containing about
25,000 template fragments from 578 different source structures. Based
on this library, we semi-automatically model selected RNA structures,
achieving 70% coverage of the native structure of an RNAse P A-type S
domain. In addition, we present implementational details for a
semi-automatic modeling framework employing an RNA sequence-structure
alignment and an alignment validation method via isostericity
matrices. The framework is tested on sample hairpin and tRNA
targets. The results of this thesis demonstrate that building a target
structure based on structure fragments from different template
structures is a feasible approach for the RNA structure modeling and
prediction problem.


DOWNLOAD: pdf (~2MB)

B.Sc. Thesis: Application of a Combined Sequence and Structure Alignment for RNA 3D Modeling

ABSTRACT:

  The prediction of RNA structure is a major field of bioinformatics research. 
  A framework for modeling RNA 3D structures based on sequence-to-structure alignment 
  via genetic algorithm (RAGA) has been designed in a previous work. Due to performance 
  and robustness problems with the RAGA algorithm it has to be exchanged with 
  a newly developed method: Lagrangian Relaxed RNA structure alignment (LR-RSA). 
  This thesis describes the necessary modifications which had to be applied to 
  the framework to embed the new alignment and restore the operative status of 
  the RNA Threading Framework. Also a validation is given whether the new algorithm 
  is an acceptable replacement within the RNA 3D structure prediction. 


DOWNLOAD: pdf (~3MB)