Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach
Fig 6
Best solution obtained by unbound fragment docking, chain-propensity filtering, and poses clustering.
For 1B7F (A) or 1CVJ (B), the best prediction (in RMSD) for each fragment in frag1-5, out of a total of ~300 poses for the whole complex (small beads), is superimposed to the bound form of the RNA (sticks and large beads). The orientation of each nucleotide is distinguishable by colors: backbone in orange, sugar in green and base in blue. For clarity, the nucleotides are in an ultra-coarse grained representation, with three bead for the base, the sugar and the phosphate.