Publications

Search for Rhiju Das' papers on PubMed

32. 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. Link

31. 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. Link

30. 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 . Link

29. 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. Link

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

27. 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 Link.

26. Fenn, R.M., Das, R., and Harbury, P.B. (2008) "Remeasuring the double helix", Science, 322, 446-449. 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.

25. 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. Link

24. 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. Link

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

22. 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", Proceedings of the National Academy of Sciences U.S.A 105, 4144-4149. (Track II) Link

21. 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. Link[highlighted in Dodson, E., "News and Views, computational biology: protein predictions", Nature 450, 176-177.]

20. 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. Link

19. 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. (Track II) Link

18. 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.

17. 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.

16. 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.

15. 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.

14. 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.

13. 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. (Track II)

12. 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.

11. 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.

10. 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.

9. 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.

8. 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.

7. 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.

6. 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.

5. 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.

4. 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.

3. 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.

2. 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.

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