X3DNA-DSSR: a resource for structural bioinformatics of nucleic acids

X3DNA-DSSR is a unique resource that excels in structural bioinformatics of nucleic acids. The proposed resource builds upon the features and large user base of 3DNA and DSSR enabled by the grant R01GM096889 on “Continued Development and Maintenance of the 3DNA Suite of Programs” (June 2011 to August 2020). DSSR was created using a bottom-up, systematic approach, with sustainability and usability in mind. It greatly expands the capabilities of 3DNA, allowing for the analysis of non-canonical DNA and RNA structures, and their interactions with proteins in a consistent framework. The single DSSR program (rather than a suite of programs as in 3DNA) is written entirely in strict ANSI C, is self- contained, and has no external dependencies. DSSR has been incorporated into numerous bioinformatics resources and research pipelines. The PI has continuously maintained the 3DNA Forum for nearly 20 years. The Forum currently has ~5400 members from all over the world and is spam-free. Because of his intimate knowledge of the entire code base of 3DNA and DSSR, the PI can quickly resolve problems reported by users. Since 2018, representative 3DNA/DSSR papers have been cited in 769 articles, published in 221 different peer-reviewed journals from scientists in 66 different fields. NIGMS is the top NIH funding Institute that has supported these articles. This R24 grant proposal aims to: (i) Maintain and refine 3DNA/DSSR to keep the resource state-of-the-art, (ii) Increase accessibility of the resource to a larger user community, and (iii) Identify and annotate G-quadruplexes and DNA-protein interactions. The proposed resource will have a broad and significant impact on the structural biology community by incorporating DSSR annotations into the NAKB, Jmol, and PyMOL.