RNA structures in RNA-Puzzles are deposited as PDB format. However, we need to consider the variations when participants generate their predictions, e.g. the nomencleture of the residue/atom names, and the variations in the format of deposited native structure. Sometimes, the sequence used in prediction may slightly deviate from the solved crystal structure: in such a case, we need to compare only the common part of the structure.
Considering these aspects, we provide some tools here to normalize the PDB format of RNA structure:
– this tool is the PDB normalization tool used by RNA-Puzzles, and is part of the basic assessment metrics tool. (Maintained by Chichau)
– Alternatively, you may use a more functional tool RNA-PDB-tools, which is mained by Marcin Magnus.