Publications & Preprints

Search for papers from the Das Lab on PubMed

Seetin, M.G., Kladwang, W., Bida, J.P., and Das, R. (2013) "Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol", Meth. Mol. Biol., in press. Preprint.

Cordero, P., Kladwang, W., VanLang, C.C., and Das, R. (2013) "A mutate-and-map protocol for inferring base pairs in structured RNA", Meth. Mol. Biol., in press. Preprint.

Sripakdeevong, P., Cevec, M., Chang, A.T., Erat, M.C., Ziegeler, M., Zhao, Q., Fox, G.E., Gao, X., Kennedy, S.D., Kierzek, R., Nikonowicz, E.P., Schwalbe, H., Sigel, R.K.O., Turner, D.H. and Das, R. (2013) "Consistent structure determination of noncanonical RNA motifs from ¹H NMR chemical shift data". Preprint.

Kim, H., Cordero, P., Das, R., Yoon, S. (2013) "HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis", Nucleics Acid Res., doi: 10.1093/nar/gkt501. Paper. Link. Server

. Das, R. (2013) "Atomic-accuracy prediction of protein loop structures enabled by an RNA-inspired ansatz". Preprint

Lyskov, S., Chou, F.-C., Ó Conchúir, S., Der, B.S., Drew, K., Kuroda, D., Xu, J., Weitzner, B.D., Renfrew, P.D., Sripakdeevong, P., Borgo, B., Havranek, J.J., Kuhlman, B., Kortemme, T., Bonneau, R., Gray, J.J., and Das, R. (2013) "Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE)". PLoS One 8(5): e63906. Paper. Link. Servers.

Adams, P.D., Baker, D., Brunger, A.T., Das, R., DiMaio, F., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C. (2013) "Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems", Ann. Rev. Biophys. Link. Paper.

Molski, M.A., Goodman, J.L, Chou, F-C., Baker, D., Das, R. and Schepartz, A. (2013) "Remodeling a beta-peptide bundle", Chemical Science, 4: 319-324. Paper. Link. Design server.

Chou, F.-C., Sripakdeevong, P., Dibrov, S.M, Hermann, T. and Das, R. (2013) "Correcting pervasive errors in RNA crystallography through enumerative structure prediction", Nature Methods, 10: 74-76. Paper. Link. ERRASER Server.

Cordero, P., Lucks, J., and Das, R. (2012) "An RNA Mapping Database for curating RNA structure mapping experiments", Bioinformatics, 28: 3006-3008. Paper. Link. Database.

Cordero, P., Kladwang, W., VanLang, C.C., and Das. R. (2012) "Quantitative dimethyl sulfate (DMS) mapping for automated RNA secondary structure inference", Biochemistry, 51: 7037-7039 Paper. Link.

Kladwang, W., Hum, J., and Das, R. (2012) "Ultraviolet shadowing of RNA can cause significant chemical damage in seconds", Scientific Reports, 2: Article 517. Paper. Link

Bida, J.P. and Das, R. (2012) "Squaring theory with practice in RNA design", Current Opinion in Structural Biology, 22: 457-466. Paper. Link.

Sripakdeevong, P., Beauchamp, K., Das, R. (2012). "Why can't we predict RNA structure at atomic resolution?" in RNA 3D Structure Analysis and Prediction, eds. Leontis, N. and Westhof, E., Nucleic Acids and Molecular Biology 27: 43-65. Paper. Link.

Beauchamp, K., Lin, Y-S., Das, R., and Pande. V.S. (2012) "Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements", J. Comp. Theor. Chem., 8 (4): 1409-1414 Paper. Link.

Frederiksen, J.K., Li, N.S., Das, R., Herschlag, D., and Piccirilli, J.A. (2012) "Metal-ion rescue revisited: Biochemical detection of site-bound metal ions important for RNA folding", RNA, 18: 1123-41. Paper. Link.

Cruz, J.A., Blanchet, M., Boniecki, M., Bujnicki, J., Chen, S-J., Cao, S., Das, R., Ding, F., Dokholyan, N.V., Flores, S.C., Huang, L., Lavender, C.A., Lisi, V., Major, F., Mikolajczak, K., Patel, D.J., Philips, A., Puton, T., Santalucia, J., Sijenyi, F., Hermann, T., Rother, K., Rother, M., Serganov, A., Skorupski, M., Soltysinski, T., Sripakdeevong, P., Tuszynska, I., Weeks, K.M., Waldsich, C., Wildauer, M., Leontis, N.B., and Westhof, E. (2012) "RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction", RNA, 18:610-25. Paper. Link.

Kladwang, W., Chou, F.-C., and Das, R. (2012) "Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches", J. Am. Chem. Soc. 134 (3):1404-1407. Paper. Link. Models.

Sripakdeevong, P., Kladwang, W., and Das, R. (2011) "An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling", Proc. Natl. Acad. Sci. U.S.A 108:20573-20578. Paper Link.

Kladwang, W., VanLang, C.C., Cordero P., and Das, R. (2011) "A two-dimensional mutate-and-map strategy for non-coding RNA structure", Nature Chemistry 3: 954-962. Paper. Link.

Kladwang, W., VanLang, C.C., Cordero P., and Das, R. (2011) "Understanding the errors of SHAPE-directed RNA structure modeling". Biochemistry 50(37):8049-8056 Paper. Link.

Beauchamp K.A., Ensign D.L., Das R., and Pande V.S. (2011). "Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments", Proc. Natl. Acad. Sci. U.S.A., 108:12734-9. Paper. Link.

Das, R. (2011). "Four small puzzles that Rosetta doesn't solve". PLoS One, 6(5):e20044 Paper. Link.

Yoon, S., Kim, J., Hum, J., Kim, H., Park, S., Kladwang, W., and Das, R. (2011). "HiTRACE: High-throughput robust analysis for capillary electrophoresis", Bioinformatics, 27(13):1798-805. Paper. Link. Software. Online documentation.

Rocca-Serra P., Bellaousov S., Birmingham A., Chen C., Cordero P., Das R., Davis-Neulander L., Duncan C.D., Halvorsen M., Knight R., Leontis N.B., Mathews D.H., Ritz J., Stombaugh J., Weeks K.M., Zirbel C.L., Laederach A. (2011). "Sharing and archiving nucleic acid structure mapping data." RNA 17(7):1204-12. Paper. Link.

Kladwang, W., Cordero P., and Das, R. (2011). "A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA". RNA 17:522-534. Paper. Link.

Leaver-Fay, A., Tyka, M., Lewis, S.M., Lange, O.F., Thompson, J. Jacak, R., Kaufmann, K.W., Renfrew, P.D., Smith, C.A., Sheffler, W., Davis, I.W., Cooper, S., Treuille, A., Mandell, D.J., Richter, F., Ban, YE., Fleishman, S.J., Corn, J.E., Kim, D.E., Lyskov, S., Berrondo, M., Mentzer, S., Popovic, Z., Havranek, J.J., Karanicolas, J., Das, R., Meiler, J., Kortemme, T., Gray, J.J., Kuhlman, B., Baker, D., Bradley, P. (2011). "ROSETTA3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules". Methods in Enzymology, 487: 545-574. Paper. Link.

Kladwang, W. and Das, R. (2010). "A mutate-and-map strategy for inferring base pairs in structured nucleic acids: proof of concept on a DNA/RNA helix". Biochemistry 49:7414-6. Paper. Link.

Fleishman S.J., Corn J.E., Strauch E.M., Whitehead T.A., Andre I., Thompson J., Havranek J.J., Das R., Bradley P., Baker D. (2010). "Rosetta in CAPRI rounds 13-19". Proteins 78, 15. Paper. Link.

Das, R., Karanicolas, J., Baker., D (2010). "Atomic accuracy in predicting and designing noncanonical RNA structure". Nature Methods 7:291-294. Paper. Link. Server. Models.

Previous work by R. Das

Das, R., Andre, I., Shen, Y,, Wu, Y., Lemak, A., Bansal, S., Arrowsmith, C.H., Szyperski, T., Baker, D. (2009). "Simultaneous prediction of protein folding and docking at high resolution". Proc. Natl. Acad. Sci. U.S.A.106:18978-83. Paper. Link.

Raman, S., Vernon, R., Thompson, J., Tyka, M., Sadreyev, R., Pei, J., Kim, D., Kellogg, E., DiMaio, F., Lange, O., Kinch, L., Sheffler, W., Kim, B.H., Das, R., Grishin, N.V., Baker, D. (2009). "Structure prediction for CASP8 with all-atom refinement using Rosetta." Proteins. 77: S89-99. Paper. Link.

Kim, J., Yu, S., Shim, B., Kim, H., Min, H., Chung, E-Y., Das, R., and Yoon S. (2009). "A robust peak detection method for RNA structure inference by high-throughput contact mapping", Bioinformatics 25: 1137-44. Paper. Link.

Schwede T., Sali, A., Honig, B., Levitt, M., Berman, H.M., Jones, D., et al. (2009). "Outcome of a workshop on applications of protein models in biomedical research", Structure 17: 151-9. Paper. Link.

Das, R. and Baker, D. (2009). "Prospects for de novo phasing with protein de novo models". Acta Cryst., D65: 169-175. Paper. Link.

Jonikas, M.A., Radmer, R.J., Laederach, A., Das R., Pearlman, S., Herschlag D., and Altman, R.B. (2009), "Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters", RNA 15:189-199. Paper. Link.

Fenn, R.M., Das, R., and Harbury, P.B. (2008). "Remeasuring the double helix", Science, 322, 446-449. Paper. Link.
   See also: Fenn, R.M., Das, R., Fenn, T.D., Schneiders, M., and Harbury, P.B. "Response to Comment on 'Remeasuring the double helix'", 325: 538. Link.

Fenn, R.M., Das, R., Silverman, J.A., Fenn, T.D., Walker, P. and Harbury, P.B.(2008). "An X-ray molecular ruler for measuring quantitative distance distributions in solution", PLoS One,3: e3229. Paper. Link.

Laederach, A., Das, R., Vicens, Q., Pearlman, S., Brenowitz, M., Herschlag, D., and Altman, R.B. (2008). "Semi-automated and rapid quantification of nucleic acid footprinting and structure mapping experiments", Nature Protocols, 3: 1395-401. Paper. Link.

Das, R. and Baker, D. (2008). "Macromolecular modeling with Rosetta", Annual Review of Biochemistry 77, 363-382. Paper. Link.

Das, R., Kudaravalli, M., Jonikas, M., Laederach, A., Fong, R., Schwans, J.P., Baker, D., Piccirilli, J.A., Altman, R.B., and Herschlag, D. (2007). "Structural inference of native and partially folded RNA by high throughput contact mapping", Proc. Natl. Acad. Sci. U.S.A 105, 4144-4149. Paper. Link. Scripts.

Qian, B., Raman, V.S., Das, R., Bradley, P., McCoy, A.J., Read, R.J., Baker, D. (2007). "High resolution structure prediction and the crystallographic phase problem", Nature 450, 259-264. Paper. Link.

Das, R., Qian, B., Raman, V.S., Vernon, R., Thompson, J., Bradley, P., Khare, S., Tyka, M., Bhat, D., Chivian, D.C., Kim, D.E., Sheffler, W., Malmstrom, L., Wollacott, A., Wang, C., Andre, I., and Baker, D. (2007). "Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home", Proteins 69, S118-128. Paper. Link.

Das, R. and Baker, D. (2007). "Automated de novo prediction of native-like RNA tertiary structures", Proceedings of the National Academy of Sciences U.S.A. 104, 14644"14669. Paper. Link. Models.

Blum, B., Jordan, M.I., Kim, D., Das, R., Bradley, P., and Baker, D. (2007). "Feature selection methods for improving protein structure prediction with Rosetta", in Advances in Neural Information Processing Systems (NIPS) 21, eds. Platt, J., Koller, D., Singer, Y., and McCallum, A., MIT Press. Paper. Link.

Lipfert, J., Das, R., Chu, V.B., Kudaravalli, M., Boyd, N., Herschlag, D. and Doniach, S. (2007). "Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae", Journal of Molecular Biology 365, 1393-1406. Paper. Link.

Russell, R., Das, R., Suh, H., Travers, K., Laederach, A., Engelhardt, M., and Herschlag D. (2006). "The paradoxical behavior of a highly structured misfolded intermediate in RNA folding", Journal of Molecular Biology 363, 531-544. Paper. Link.

Das, R. and Doniach, S. (2006). "Structural studies of proteins and nucleic acids in solution using small angle x-ray scattering (SAXS)," in Soft Matter: Scattering, Imaging and Manipulation, eds. Pecora, R. and Borsali, R., Kluwer Press. Paper.

Das, R., Travers, K.J., Bai, Y., and Herschlag, D. (2005). "Determining the Mg²⁺ stoichiometry for folding an RNA's metal ion core", Journal of the American Chemical Society 127, 8272-8273. Paper. Link.

Bai, Y., Das, R., Millett, I.S., Herschlag, D., and Doniach, S. (2005). "Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution." Proceedings of the National Academy of Sciences U.S.A. 102, 959-960. Paper. Link.

Das, R., Laederach, A., Pearlman, S.M., Herschlag, D., and Altman, R.B. (2005). "SAFA: Semi-Automated Footprinting Analysis software for high-throughput quantification of nucleic acid footprinting experiments." RNA 11, 344-354. Paper. Link. Software.

Andresen, K., Das, R., Park, H.Y., Smith, H., Kwok, L.W., Lamb, J.S., Kirkland, E.J., Herschlag, D., Finkelstein, K.D., and Pollack, L. (2004). "Spatial distribution of competing ions around DNA in solution." Physical Review Letters 93, 248013. Paper. Link.

Takamoto, K., Das, R., He, Q., Doniach, S., Brenowitz, M., Herschlag, D., and Chance, M. (2004). "Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations." Journal of Molecular Biology 343, 1195-206. Paper. Link.

Das, R., Kwok, L.W., Millet, I.S., Bai, Y., Mills, T.T., Jacob, J., Maskel, G.S., Seifert, S., Simon, M.G.J., Thiyagarajan, P., Doniach, S., Pollack, L., and Herschlag, D. (2003). "The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme." Journal of Molecular Biology 332, 311-319. Paper. Link.

Das, R., Mills, T.T., Kwok, L.W., Maskel, G.S., Millett, I.S., Doniach, S., Finkelstein, K.D., Herschlag, D. and Pollack, L. (2003). "The counterion distribution around DNA probed by solution x-ray scattering." Physical Review Letters 90, 188103. Paper. Link.

Bartley, L., Zhuang, X., Das, R., Chu, S., and Herschlag, D. (2003). "Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA." Journal of Molecular Biology 328, 1011-1026. Paper. Link.

Saunders, R., Kneissl, R., Grainge, K., Grainger, W.F., Jones, M.E., Maggi, A., Das,R., Edge, A.C., Lasenby, A.N., Pooley, G.G., Shigeru, J.M., Tsuruta, T., Yamashita, K., Tawara, Y., Furuzawa, A., Harada, A., and Hatsukade I. (2003). "A measurement of H0 from Ryle Telescope, ASCA and ROSAT observations of Abell 773." Monthly Notices of the RoyalAstronomical Society 341, 937-940. Paper. Link.

Grainger, W.F., Das, R., Grainge, K., Jones, M. E., Kneissl, R., Pooley, G.G., and Saunders, R.D.E. (2002). "A maximum-likelihood approach to removing radio sources from observations of the Sunyaev-Zel'dovich effect, with application to Abell 611." Monthly Notices of the Royal Astronomical Society 337, 1207-1214. Paper. Link.

Cotter, G., Buttery, H.J., Das, R., Jones, M.E., Grainge, K., Pooley, G.G, and Saunders, R. (2002). "Observations of the Sunyaev-Zel'dovich effect in the z = 0.78 cluster MS 1137.5+6625." Monthly Notices of the Royal Astronomical Society 334, 323-326. Paper. Link.

Cotter G., Buttery, H.J., Rawlings, S., Croft, S., Hill, G.J., Gay, P., Das, R., Drory, N., Grainge, K., Grainger, W.F., Jones, M.E., Pooley, G.G., and Saunders, R. (2002). "Detection of a cosmic microwave background decrement towards a cluster of mJy radio sources." Monthly Notices of the Royal Astronomical Society 331, 1-6. Paper. Link.

Das, R., "Theoretical Basis of Likelihood Methods in Molecular Phylogenetic Inference", M. Res. Thesis, Dept. of Biology, University College London. Supervisors: Z. Yang & J. Mallet. Manuscript.

Alba, M.M., Das, R., Orengo, C.A., and Kellam, P. (2001). "Genomewide function conservation and phylogeny in the Herpesviridae." Genome Research 11, 43-54. Paper. Link.

Das, R., "Analysis of Sunyaev-Zel'dovich Decrements", M. Phil. Thesis, Dept. of Physics, Cambridge University. supervisor: R. Saunders. Manuscript.

Milton, K. and Das, R. (1996). "Finite element lattice Hamiltonian matrix elements. Anharmonic oscillators." Letters in Mathematical Physics 36, 177-187. Paper. Link.