Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity

Background: Computational comparison of two protein structures is the starting point of many methods that build on existing knowledge, such as structure modeling (including modeling of protein complexes and conformational changes), molecular replacement, or annotation by structural similarity. In a commonly used strategy, significant effort is invested in matching two sets of atoms. In a complementary approach, a global descriptor is assigned to the overall structure, thus losing track of the substructures within. Results: Using a small set of geometric features, we define a reduced representation of protein structure, together with an optimizing function for matching two representations, to provide a pre-filtering stage in a database search. We show that, in a straightforward implementation, the representation performs well in terms of resolution in the space of protein structures, and its ability to make new predictions. Conclusions: Perhaps unexpectedly, a substantial discriminatin...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Zong Hong Zhang, Hwee Kuan Lee, Ivana Mihalek
• Keywords: BMCBI 2010, Protein Complexes, Protein Structures, Secondary Structural Element