Research Topics
| Rhiju DasSummaryAffiliation: University of Washington Country: USA Publications
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Publications
Macromolecular modeling with rosettaRhiju Das
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Annu Rev Biochem 77:363-82. 2008..Emerging connections to crystallographic phasing, NMR modeling, and lower-resolution approaches are described and critically assessed...- Prospects for de novo phasing with de novo protein modelsRhiju Das
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Acta Crystallogr D Biol Crystallogr 65:169-75. 2009..Improvements in conformational search methods will be necessary if molecular replacement with de novo models is to become a practical tool for targets without homology to previously solved protein structures... - High-resolution structure prediction and the crystallographic phase problemBin Qian
University of Washington, Department of Biochemistry and Howard Hughes Medical Institute, Box 357350, Seattle 98195, USA
Nature 450:259-64. 2007.... - Rosetta in CAPRI rounds 13-19Sarel J Fleishman
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Proteins 78:3212-8. 2010..Analysis of our failures in the CAPRI challenges suggest that conformational sampling at the termini of exposed beta strands is a particularly pressing area for improvement... - Structure prediction for CASP8 with all-atom refinement using RosettaSrivatsan Raman
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Proteins 77:89-99. 2009..These improvements over the starting template-based models and refinement tests demonstrate the power of Rosetta structure refinement in improving model accuracy... - A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNAWipapat Kladwang
Department of Biochemistry, Stanford University, Stanford, California 94305, USA
RNA 17:522-34. 2011..These results establish the accuracy and information content of the mutate-and-map strategy and support its feasibility for rapidly characterizing the base-pairing patterns of larger and more complex RNA systems... - Simultaneous prediction of protein folding and docking at high resolutionRhiju Das
Department of Biochemistry, University of Washington, Seattle WA 98195, USA
Proc Natl Acad Sci U S A 106:18978-83. 2009.... - Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@homeRhiju Das
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Proteins 69:118-28. 2007..These results indicate that refinement with an all-atom energy function, although computationally expensive, is a powerful method for obtaining accurate structure predictions... - ROSETTA3: an object-oriented software suite for the simulation and design of macromoleculesAndrew Leaver-Fay
Department of Biochemistry, University of North Carolina, Chapel Hill, North Carolina, USA
Methods Enzymol 487:545-74. 2011..This chapter describes the requirements for our new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform... - Automated de novo prediction of native-like RNA tertiary structuresRhiju Das
Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Box 357350, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 104:14664-9. 2007.... - A two-dimensional mutate-and-map strategy for non-coding RNA structureWipapat Kladwang
Department of Biochemistry, Stanford University, Stanford, California 94305, USA
Nat Chem 3:954-62. 2011..7 Å) of an adenine riboswitch. These results establish a promising two-dimensional chemical strategy for inferring the secondary and tertiary structures that underlie non-coding RNA behaviour... - Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solutionYu Bai
Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 102:1035-40. 2005..An upper limit on the magnitude of the attractive potential under all tested ionic conditions is estimated... - Understanding the errors of SHAPE-directed RNA structure modelingWipapat Kladwang
Department of Biochemistry, Stanford University, Stanford, California 94305, USA
Biochemistry 50:8049-56. 2011..Thus, SHAPE-directed RNA modeling is not always unambiguous, and helix-by-helix confidence estimates, as described herein, may be critical for interpreting results from this powerful methodology... - A mutate-and-map strategy for inferring base pairs in structured nucleic acids: proof of concept on a DNA/RNA helixWipapat Kladwang
Department of Biochemistry, Stanford University, Stanford, California 94035, USA
Biochemistry 49:7414-6. 2010..These results point to the feasibility of rapid base pair inference in larger and more complex nucleic acid systems with unknown structure... - A molecular ruler for measuring quantitative distance distributionsRebecca S Mathew-Fenn
Department of Biochemistry, Stanford University, Stanford, California, USA
PLoS ONE 3:e3229. 2008..The X-ray scattering interference ruler should be a powerful tool for relating crystal structures to solution structures and for studying molecular fluctuations... - Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitchesWipapat Kladwang
Department of Biochemistry, Stanford University, Stanford, California 94305, USA
J Am Chem Soc 134:1404-7. 2012..We speculate that several further undiscovered elements are likely to exist in the flanking regions of this and other functional RNAs, and automated prediction tools can play a useful role in their detection and dissection... - Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNALaura E Bartley
Department of Biochemistry, B400 Beckman Center, Stanford University, Stanford, CA 94305-5307, USA
J Mol Biol 328:1011-26. 2003..The results described here, combined with previous work, provide an in-depth view of an RNA tertiary structure formation event and suggest that large, highly structured RNAs may have local regions that are misordered... - SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experimentsRhiju Das
Department of Physics, Stanford University, Stanford, CA 94305, USA
RNA 11:344-54. 2005..Further, the increased throughput provided by SAFA may allow a more comprehensive understanding of molecular interactions. The software and documentation are freely available for download at http://safa.stanford.edu... - The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozymeRhiju Das
Department of Physics, Stanford University, Stanford, CA 94305-4060, USA
J Mol Biol 332:311-9. 2003..These results help delineate an analogy between the early conformational changes in RNA folding and the "burst phase" changes and molten globule formation in protein folding... - Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cationsKeiji Takamoto
Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, New York, NY 10461, USA
J Mol Biol 343:1195-206. 2004..The folding model derived from these and previous results provides a robust framework for understanding the equilibrium and kinetic folding of RNA... - Determining the Mg2+ stoichiometry for folding an RNA metal ion coreRhiju Das
Department of Physics and Biochemistry, Stanford University, Stanford, CA 94305, USA
J Am Chem Soc 127:8272-3. 2005..By pinpointing the metal ion stoichiometry, these measurements provide a critical but previously missing step in the thermodynamic dissection of the coupling between metal ion binding and RNA folding... - The paradoxical behavior of a highly structured misfolded intermediate in RNA foldingRick Russell
Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
J Mol Biol 363:531-44. 2006..We speculate that the complex topology of RNA secondary structures and the inherent rigidity of RNA helices render kinetic traps due to topological isomers considerably more common for RNA than for proteins... - Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio choleraeJan Lipfert
Department of Physics, Stanford University, Stanford, CA 94305, USA
J Mol Biol 365:1393-406. 2007..These data provide a first glimpse into the structural conformations of the VCI-II aptamer, establish rigorous constraints for further modeling, and provide a framework for future mechanistic studies... - Structural inference of native and partially folded RNA by high-throughput contact mappingRhiju Das
Departments of Biochemistry, Bioengineering, and Genetics, Stanford University, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 105:4144-9. 2008..With its applicability to nearly any solution state, we expect MOHCA to be a powerful tool for illuminating the many functional structures of large RNA molecules and RNA/protein complexes... - Remeasuring the double helixRebecca S Mathew-Fenn
Biophysics Program, Stanford University, Stanford, CA 94305, USA
Science 322:446-9. 2008..Our observations support the idea of long-range allosteric communication through DNA structure...