De novo 3D models of SARS-CoV-2 RNA elements and small-molecule-binding RNAs to guide drug discovery

Ramya Rangan; Andrew M. Watkins; Wipapat Kladwang; Rhiju Das

For each target, FARFAR2 simulations were executed as previously described, 10 providing sequence and secondary structure information to the rna_denovo application provided with Rosetta 3.12. Clustering was achieved via the rna_cluster application, examining the top 400 structures by energy with a cluster radius of 5.0 or 2.0 Å depending on the structural element as described above. Specifically, the rna_cluster application iterates through unclustered structures from best to worst energy, either assigning them to an existing cluster center (if the all-heavy-atom RMSD of the model is within the clustering radius of the cluster center) or starting a new cluster. Homology modeling with FARFAR2 for the 5′ UTR SL2 and the 3′ UTR stem-loop II-like motif (s2m) was carried out using the approach outlined in ref. 26 For the 5′ UTR SL2, PDB ID 2L6I 4 was used as a template for positions 45 to 59. For the 3′ UTR s2m, PDB ID 1XJR 5 was used as a template for positions -144 to -104; here, nucleotide numbering maps to the 3′ UTR secondary structure in Fig. 4 .