![]() Moreover, the January 2022 issue of RNA continues to highlight DSSR-enabled schematics (see the note below). The DSSR-PyMOL schematics have been featured in all 12 cover images (January to December) of the RNA Journal in 2021. Recommended in Faculty Opinions: “simple and effective”, “Good for Teaching”.Įmployed by the NDB to create cover images of the RNA Journal. Color code for base blocks: A, red C, yellow G, green T, blue U, cyan G-tetrad, green WC-pairs, per base in the leading strand. Watson-Crick pairs are shown as long blocks with minor-groove edges in black (A, B), G-tetrads represented as square blocks and the metal ion as sphere ©, the ligand rendered as balls-and-sticks (D), and proteins depicted as purple cartoons (E, F). Innovative cartoon-block schematics enabled by the DSSR-PyMOL integration for six representative PDB entries. Here are two chromatin-like models using PDB entry 4xzq as the template.Ĭircular DNA duplexes modeled using DSSR Pro.ĭNA super helices modeled using DSSR Pro. Template-based modeling of DNA-protein complexes using DSSR Pro. Theoretical models of G-quadruplexes, created using DSSR Pro. DSSR requires no set up or configuration: it simply works. It is also routinely checked with Valgrind to avoid memory leaks. DSSR has been extensively tested using all nucleic-acid-containing structures in the PDB. The binary executables for macOS, Linux, and Windows are just ~2MB. It is self-contained, with zero runtime dependencies on third-party libraries. It is written in strict ANSI C, as a single command-line program. DSSR is a solid software product that excels in RNA structural bioinformatics. Moreover, DSSR Pro includes an in-depth user manual and one-year technical support from the developer. For example, with the mutate module of DSSR Pro, one can automatically perform the following tasks: (i) mutate all bases to Us, (ii) mutate bases in hairpin loops to Gs, and (iii) mutate G–C Watson-Crick pairs to C–G, and A–U to U–A. It integrates the disparate analysis and modeling programs of 3DNA under one umbrella, and offers new advanced features, through a convenient interface. It has more functionalities than DSSR basic (the free academic version), including: (i) homology modeling via in silico base mutations, a feature employed by Merck scientists, (ii) easy generation of regular helical models, including circular or super-helical DNA (see figures below), (iii) creation of customized structures with user-specified base sequences and rigid-body parameters, (iv) efficient processing of molecular dynamics (MD) trajectories, (v) detailed characterization of DNA-protein or RNA-protein spatial interactions, and (vi) template-based modeling of DNA-protein complexes (see figures below). DSSR may be licensed from Columbia University. DSSR has also been adopted into numerous other structural bioinformatics resources, including: (i) URS, (ii) RiboSketch, (iii) RNApdbee, (iv) forgi, (v) RNAvista, (vi) VeriNA3d, (vii) RNAMake, (viii) ElTetrado, (ix) DNAproDB, (x) LocalSTAR3D, (xi) IPANEMAP, and (xii) RNANet.Īdvanced features. The DSSR-Jmol and DSSR-PyMOL integrations bring unparalleled search capabilities (e.g., ‘select junctions’ for all multi-branch loops) and innovative visualization styles into 3D nucleic acid structures. To make DSSR as widely accessible as possible, I have initiated collaborations with the principal developers of Jmol and PyMOL. Shaw Research), (iv) “Predicting site-binding modes of ions and water to nucleic acids using molecular solvation theory” ( JACS, 2019), (v) “RIC-seq for global in situ profiling of RNA- RNA spatial interactions” ( Nature, 2020), and (vi) “DNA mismatches reveal conformational penalties in protein- DNA recognition” ( Nature, 2020).īroad integrations. DSSR has been widely cited in scientific literature, including: (i) “Selective small-molecule inhibition of an RNA structural element” ( Nature, 2015 Merck Research Laboratories), (ii) “The structure of the yeast mitochondrial ribosome” ( Science, 2017), (iii) “RNA force field with accuracy comparable to state-of-the-art protein force fields” ( PNAS, 2018 D. ![]() It streamlines tasks in RNA/DNA structural bioinformatics, and outperforms its ‘competitors’ by far in terms of functionality, usability, and support. DSSR has been made possible by the developer’s extensive user-support experience, detail-oriented software engineering skills, and expert domain knowledge accumulated over two decades. It is built upon the well-known, tested, and trusted 3DNA suite of programs. DSSR (Dissecting the Spatial Structure of RNA) is an integrated software tool for the analysis/annotation, model building, and schematic visualization of 3D nucleic acid structures (see the figures below and the video overview). ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |