Structural biology operates robust tools and data for proteins; the field of nucleic acid (NA) structure analysis and prediction lags behind. This is serious for RNA structures in the context of the ability to predict their variable 3D structures and for DNA for understanding of their mutual recognition with proteins. More reliable prediction of RNA 3D structures is primarily hindered by a scarcity of sequence alignments of functionally wide spectrum of RNAs. A better understanding of both RNA and DNA could be much more profound if more high-quality structures were available, and the quality of the existing structures was gauged more reliably [1]. Our work addresses the latter, improving the quality of the existing NA structures and methods of their analysis. Current challenges in NA structure quality include: (A) Inconsistent application of valence geometry restraints. (B) Poorly refined backbone conformations. (C) Incomplete or incorrect base pairing assignments. This presentation will introduce key features of fully redesigned DNATCO version 5.0 at dnatco.datmos.org [2], a suite of web-based tools designed to enhance NA structure annotation and validation. DNATCO includes:
An Annotation TAB for clear structural overviews. Quite significantly, the new DNATCO provides full annotation of base pairs in the Leontis-Westhof classification schema [3] both in tabular form and - to the best of our knowledge - for the first time as an integrated part of molecular graphics.
A Validation TAB offering detailed analysis, including dinucleotide conformation analysis (based on our NtC classification [4]), novel RMSD/RSCC scatterplots, and detailed valence geometry evaluation.
A Browse TAB for multi-view structure visualization.
Our ongoing development aims to provide tools for direct structure modification during the refinement process, further contributing to higher-quality NA structural data.
This research was funded by Czech Academy of Sciences, grant RVO 86652036 and by grant LM2023055 to ELIXIR CZ from MEYS Czech Republic.