MOESM2 of RNA 3D structure prediction guided by independent folding of homologous sequences

Additional file 2: The analysis was performed also for various combinations of sequences of homologs (related to Fig. 6). The results of an analysis of core RMSD of all possible combinations of five input sequences of homologs for all 8 RNA families investigated in this work: Adenine riboswitch (Ade), c-di-GMP riboswitch (GMP), TPP riboswitch (TPP), THF riboswitch (THF), tRNA, RNA-Puzzle 13 (RP13), RNA-Puzzle 14 (RP14), RNA-Puzzle 17 (RP17). This analysis was performed with the evox_all_variants.py from the EvoClustRNA package. Each sequence of homologs was ordered from 1 to 3. A mode “h1” means models of the first homolog and the target sequence used for clustering, “h2” means models of the second homolog and the target sequence. “h234” means that models of three homologs were considered during clustering, the second homolog, third and fourth. For each variant 5 top clusters are shown and the first cluster is marked with a black dot. The first panel combines the results for SimRNA and Rosetta, the second panel shows the results for SimRNA and the third only for Rosetta.