A novel approach is proposed for modeling of structurally variable regions in proteins. In this approach, a prerequisite sequence-structure alignment is examined for regions where the target sequence is not covered by the structural template. These regions, extended with a number of residues from adjacent stem regions, are submitted to fold recognition. The alignments produced by fold recognition are integrated into the initial alignment to create a multiple alignment where gaps in the main structural template are covered by local structural templates. This multiple alignment is used to create a protein model by existing protein modeling techniques. Several alternative parameters are evaluated using a set of ten proteins. One set of parameters is selected and evaluated using another set of 31 proteins. The most promising result is for loop regions not located at the C- or N-terminal of a protein, where the method produces an average RMSD 12% lower than the loop modeling provided with the program MODELLER. This improvement is shown to be statistically significant.
| Identifer | oai:union.ndltd.org:UPSALLA1/oai:DiVA.org:his-902 |
| Date | January 2004 |
| Creators | Levefelt, Christer |
| Publisher | Högskolan i Skövde, Institutionen för kommunikation och information, Skövde : Institutionen för kommunikation och information |
| Source Sets | DiVA Archive at Upsalla University |
| Language | English |
| Detected Language | English |
| Type | Student thesis, info:eu-repo/semantics/bachelorThesis, text |
| Format | application/postscript, application/pdf |
| Rights | info:eu-repo/semantics/openAccess, info:eu-repo/semantics/openAccess |
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