“ SLIDE ”: AN INTERACTIVE THREADING REFINEMENT TOOL FOR HOMOLOGY MODELING

Abstract

Target to template alignment is the limiting accuracy step in Homology Modeling as misalignments by only one residue may result in model errors as large as 4 Å. This step becomes even more critical when sequence identity is lower than 50% and multiple templates are not at hand for multiple alignment analysis. In these cases alignments may be improved by including structural information from the template such as by avoiding gaps in secondary structure stretches, in buried regions or between two residues that are far apart in space and to a moderate extent some newer methods take such criteria into account. However, it is always important to edit the alignment by inspecting the superposition of the target sequence onto the template structure visually, especially if the target-template sequence identity is low. To this end we have developed SLIDE – a simple tool based on Biojava and Jmol libraries that allows the interactive threading of the target onto the template, useful for changing the gap location and target sequence over the template structure and thus improving structurally the alignment by visual inspection.