报告题目: Illuminating the 3D Structure of RNA with 3DNA-DSSR
Insight into the intricate 3D architecture of RNA is essential to understanding its cellular functions. However, even small non-coding RNA molecules contain features that are overlooked by existing bioinformatics tools. DSSR (Dissecting the Spatial Structure of RNA) is an integrated tool for analyzing and annotating RNA tertiary structures, built upon the widely cited 3DNA suite of software programs. It has been created from the bottom up to streamline the characterization of 3D structure of RNA, automatically and consistently. DSSR is continuously being refined and related materials are available at http://forum.x3dna.org.
DSSR has become a de facto cornerstone tool for RNA structural bioinformatics, facilitating a broad range of applications. Specifically, DSSR is a tool that analyzes experimentally determined RNA structures, a means to collect and analyze structural features across known 3D structures, and a component of other bioinformatics resources. Notably, DSSR has been integrated into Jmol, a popular 3D molecular viewer. The DSSR-Jmol integration fills a gap in RNA structural bioinformatics, and brings 3D RNA visualization to an entirely new level. Additionally, the DSSR plugin for PyMOL allows for interactive creations of simple, yet highly revealing cartoon-block images. The DSSR-enabled PyMOL schematics will soon be featured for each DNA/RNA-containing structure in the RCSB PDB.
The talk will be based on the following two publications and recent developments of DSSR:
1．Lu et al. (2015). “DSSR: an integrated software tool for dissecting the spatial structure of RNA.” Nucleic Acids Research 43(21): e142.
2．Hanson & Lu (2017). “DSSR-enhanced visualization of nucleic acid structures in Jmol.” Nucleic Acids Research 45(W1), W528–W533.
Dr. Xiang-jun Lu is a world-leading expert in computational structural biology, specializing in the structural bioinformatics of DNA, RNA, and their complexes with proteins. He is the creator of 3DNA, a widely cited software suite that serves as the standard analysis tool for DNA double helices, and DSSR, which has quickly become a de facto computational program for the analysis and annotation of RNA 3D structures. Notably, some results from 3DNA publications have been adopted in textbooks. The DSSR-Jmol integration fills a gap in the interactive visualization of RNA structure and was highlighted as the cover image of the influential web server issue of Nucleic Acids Research (NAR) in 2017.
Created and continuously refining DSSR, integrated software for dissecting the spatial structure of RNA. DSSR has already established itself as a cornerstone tool for RNA structural bioinformatics. The program serves a broad range of applications: it is (1) a tool that analyzes experimentally determined RNA structures; (2) a component of other bioinformatics resources; and (3) a means to collect and analyze specific structural motifs across databases of known 3D structures, such as the Protein Data Bank.
Integrated DSSR into Jmol (in collaboration with Dr. Robert Hanson). This work filled a gap in RNA structural visualization, enabling interactive and sophisticated analysis of unique characteristics in novel representation styles. The DSSR-Jmol integration paper was featured as the cover image of the 2017 web issue of Nucleic Acids Research.
Created and continuously refining SNAP, an integrated software program that streamlines the characterization of 3D structures of nucleic acid-protein complexes.
Developed and currently maintaining the REDUCE suite of robust software tools that model the regulation of gene expression by transcription factors.
Created and continuously supporting the 3DNA suite of programs, which has become the standard tool for the analysis of DNA structures and DNA-protein complexes.
Resolved long-standing discrepancies in the analysis of nucleic acid structures, leading to an international standard for the description of base-pair geometry.
Devised a force field with a distributed π-charge model that successfully accounts for DNA base-stacking interactions observed in oligonucleotide X-ray crystal structures.
Improved a computer-aided identification system for X-ray powder diffraction patterns and organic mass spectra, which was commercialized and recognized by two national awards in China.
1．Hanson, R. M., & Lu*, X. J. (2017). “DSSR-enhanced visualization of nucleic acid structures in Jmol.” Nucleic Acids Research, 45(W1), W528-W533. [Featured as the cover image of the 2017 NAR web issue].
2．Waters, J. T., Lu, X. J., Galindo-Murillo, R., Gumbart, J. C., Kim, H. D., Cheatham, T. E., & Harvey, S. C. (2016). “Transitions of double-stranded DNA between the A-and B-forms.” Journal of Physical Chemistry B, 120(33), 8449–8456.
3．Waters, J. T., Kim, H. D., Gumbart, J. C., Lu, X. J., & Harvey, S. C. (2016). “DNA Scrunching in the Packaging of Viral Genomes.” Journal of Physical Chemistry B, 120(26), 6200-6207. [Featured in the American Chemical Society news article, “DNA scrunching could be new target for antiviral drugs” (June 08, 2016)].
4．Lu*, X. J., Bussemaker, H. J., & Olson, W. K. (2015). “DSSR: an integrated software tool for dissecting the spatial structure of RNA.” Nucleic Acids Research, 43(21), e142.
5．Colasanti, A. V., Lu*, X. J., & Olson, W. K. (2013). “Analyzing and building nucleic acid structures with 3DNA.” JoVE (Journal of Visualized Experiments), 74, e4401.
6．Mládek, A., Šponer, J. E., Kulhánek, P., Lu, X. J., Olson, W. K., & Šponer, J. (2011). “Understanding the sequence preference of recurrent RNA building blocks using quantum chemistry: the intrastrand RNA dinucleotide platform.” Journal of Chemical Theory and Computation, 8(1), 335-347.
7．Lu*, X. J., Olson, W. K., & Bussemaker, H. J. (2010). “The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex.” Nucleic Acids Research, 38(14), 4868-4876. [Featured in NAR as one of the best papers (top 5%) published in the journal in terms of originality, significance, and scientific excellence.]
8.Zheng, G., Lu, X. J., & Olson, W. K. (2009). “Web 3DNA—a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures.” Nucleic Acids Research, 37(W240–W246).
9.Boorsma, A., Lu, X. J., Zakrzewska, A., Klis, F. M., & Bussemaker, H. J. (2008). “Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression.” PLOS ONE, 3(9), e3112.
10．Lu*, X. J., & Olson, W. K. (2008). “3DNA: a versatile, integrated software system for the analysis, rebuilding, and visualization of three-dimensional nucleic-acid structures.” Nature Protocols, 3(7), 1213-1227.