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| Title: | The Use of Internal and External Functional Domains to Improve Transmembrane Protein Topology Prediction |
| Authors: | Xu, Wei |
| Keywords: | Computer Science
transmembrane protein
topology prediction |
| Approved Date: | 2004 |
| Date Submitted: | 2004 |
| Abstract: | Membrane proteins are involved in vital cellular functions and have important implications in disease processes, drug design and therapy. However, it is difficult to obtain diffraction quality crystals to study transmembrane protein structure. Transmembrane protein topology prediction tools try to fill in the gap between abundant number of transmembrane proteins and scarce number of known membrane protein structures (3D structure and biochemically characterized topology). However, at present, the prediction accuracy is still far from perfect. TMHMM is the current state-of- the-art method for membrane protein topology prediction. In order to improve the prediction accuracy of TMHMM, based upon the method of GenomeScan, the author implemented AHMM (augmented HMM) by incorporating functional domain information externally to TMHMM. Results show that AHMM is better than TMHMM on both helix and sidedness prediction. This improvement is verified by both statistical tests as well as sensitivity and specificity studies. It is expected that when more and more functional domain predictors are available, the prediction accuracy will be further improved. |
| Department: | School of Computer Science |
| Degree: | Master of Mathematics |
| URI: | http://hdl.handle.net/10012/1073 |
| Appears in Collections: | Electronic Theses and Dissertations (UW)
Faculty of Mathematics Theses and Dissertations
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