Topology independent comparison of RNA 3D structures using the CLICK algorithm

In this study, we extend and optimize the CLICK algorithm to superimpose pairs of RNA 3D structures and RNA–protein complexes, independent of the associated topologies. Benchmarking Rclick on four different datasets showed that it is either comparable to or better than other structural alignment methods in terms of the extent of structural overlaps. Rclick also recognizes conformational changes between RNA structures and produces complementary alignments to maximize the extent of detectable similarity. Applying Rclick to study Ribonuclease III protein correctly aligned the RNA binding sites of RNAse III with its substrate. Rclick can be further extended to identify ligand-binding pockets in RNA. A web server is developed at http://mspc.bii.a-star.edu.sg/minhn/rclick.html.

Source: Nucleic Acids Research - January 8, 2017 Category: Research Authors: Nguyen, M. N., Sim, A. Y. L., Wan, Y., Madhusudhan, M. S., Verma, C. Tags: Computational Methods Methods Online Source Type: research