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Biochemistry, Biophysics, and Structural Biology Commons

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Biostatistics

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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

A Modular Data Analysis Pipeline For The Discovery Of Novel Rna Motifs , Justin Schonfeld Jan 2006

A Modular Data Analysis Pipeline For The Discovery Of Novel Rna Motifs , Justin Schonfeld

Retrospective Theses and Dissertations

This dissertation presents a modular software pipeline that searches collections of RNA sequences for novel RNA motifs. In this case the motifs incorporate elements of primary and secondary structure. The motif search pipeline breaks up sets of RNA sequences into shortened segments of RNA primary sequence. The shortened segments are then folded to obtain low energy secondary structures. The distance estimation module of the pipeline then calculates distances between the folded bricks, and then analyzes the resulting distance matrices for patterns;An initial implementation of the pipeline is applied to synthetic and biological data sets. This implementation introduces a new ...


Distance-Based Nmr Structure Determination And Refinement, Feng Cui Jan 2005

Distance-Based Nmr Structure Determination And Refinement, Feng Cui

Retrospective Theses and Dissertations

Protein structures play a pivotal role in understanding protein functions. X-ray crystallography and nuclear magnetic resonance spectroscopy (NMR) are two main experimental approaches for protein structure determination. The structures determined by NMR are not as accurate as those by X-ray crystallography in general, due to limited distance data (e.g. NOEs) that can be generated from NMR experiments. The NMR modeling algorithms are not well developed either, to produce high-quality structures with desired accuracy and efficiency. To address the NMR modeling issues, a so-called geometric build-up approach for NMR modeling has been developed, which remarkably reduces computing time in determining ...


Study Of Secondary Structure Of Protein Sequences By Linear Algebra , Wei-Hua Hsieh Jan 1991

Study Of Secondary Structure Of Protein Sequences By Linear Algebra , Wei-Hua Hsieh

Retrospective Theses and Dissertations

Using encoding schemes, we study the relation between amino acids and protein structure in linear spaces;Local protein-structure prediction schemes use the amino acid sequences in a short subchain of a protein to predict the protein secondary structure of the middle residue of the chain;Two relatively reliable, objective and quantitative local prediction schemes are Robson et al.'s information theory method and and Qian & Sejnowski's neural network models. The latter achieved 64% accuracy for three-state predictions in 1989, the best prediction performance yet recorded;We assign to the 20 amino acids, through a one-to-one correspondence, the 20 columns (unit vectors) of the 20 x 20 identity matrix. Then any chain of k amino acids may be represented as a ...