Rhiju Das - Publications

Biochemistry and Physics Stanford University, Palo Alto, CA 
predictive understanding of how biopolymer sequences code for biopolymer structures, with an initial focus on RNA

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Year Citation  Score
2019 Magnus M, Kappel K, Das R, Bujnicki JM. RNA 3D structure prediction guided by independent folding of homologous sequences. Bmc Bioinformatics. 20: 512. PMID 31640563 DOI: 10.1186/s12859-019-3120-y  0.44
2019 Li X, Liu S, Zhang L, Issaian A, Hill RC, Espinosa S, Shi S, Cui Y, Kappel K, Das R, Hansen KC, Zhou ZH, Zhao R. A unified mechanism for intron and exon definition and back-splicing. Nature. PMID 31485080 DOI: 10.1038/s41586-019-1523-6  0.44
2019 Yesselman JD, Eiler D, Carlson ED, Gotrik MR, d'Aquino AE, Ooms AN, Kladwang W, Carlson PD, Shi X, Costantino DA, Herschlag D, Lucks JB, Jewett MC, Kieft JS, Das R. Computational design of three-dimensional RNA structure and function. Nature Nanotechnology. PMID 31427748 DOI: 10.1038/s41565-019-0517-8  1
2019 Koirala D, Shao Y, Koldobskaya Y, Fuller JR, Watkins AM, Shelke SA, Pilipenko EV, Das R, Rice PA, Piccirilli JA. A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. Nature Communications. 10: 3629. PMID 31399592 DOI: 10.1038/s41467-019-11585-z  0.6
2019 Yesselman JD, Denny SK, Bisaria N, Herschlag D, Greenleaf WJ, Das R. Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation. Proceedings of the National Academy of Sciences of the United States of America. PMID 31375637 DOI: 10.1073/pnas.1901530116  1
2019 Wu MJ, Andreasson JO, Kladwang W, Greenleaf WJ, Das R. Automated design of diverse stand-alone riboswitches. Acs Synthetic Biology. PMID 31298841 DOI: 10.1021/acssynbio.9b00142  0.6
2019 Jarmoskaite I, Denny SK, Vaidyanathan PP, Becker WR, Andreasson JOL, Layton CJ, Kappel K, Shivashankar V, Sreenivasan R, Das R, Greenleaf WJ, Herschlag D. A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins. Molecular Cell. PMID 31078383 DOI: 10.1016/j.molcel.2019.04.012  1
2019 Kappel K, Jarmoskaite I, Vaidyanathan PP, Greenleaf WJ, Herschlag D, Das R. Blind tests of RNA-protein binding affinity prediction. Proceedings of the National Academy of Sciences of the United States of America. PMID 30962376 DOI: 10.1073/pnas.1819047116  1
2018 Hartwick EW, Costantino DA, MacFadden A, Nix JC, Tian S, Das R, Kieft JS. Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels. Nature Communications. 9: 5074. PMID 30498211 DOI: 10.1038/s41467-018-07542-x  0.44
2018 Kappel K, Das R. Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking. Structure (London, England : 1993). PMID 30416038 DOI: 10.1016/j.str.2018.10.001  0.44
2018 Kappel K, Liu S, Larsen KP, Skiniotis G, Puglisi EV, Puglisi JD, Zhou ZH, Zhao R, Das R. De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes. Nature Methods. 15: 947-954. PMID 30377372 DOI: 10.1038/s41592-018-0172-2  0.44
2018 Yesselman JD, Tian S, Liu X, Shi L, Li JB, Das R. Updates to the RNA mapping database (RMDB), version 2. Nucleic Acids Research. 46: D375-D379. PMID 30053264 DOI: 10.1093/nar/gkx873  0.6
2018 Denny SK, Bisaria N, Yesselman JD, Das R, Herschlag D, Greenleaf WJ. High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding. Cell. PMID 29961580 DOI: 10.1016/j.cell.2018.05.038  1
2018 Zettl T, Das R, Harbury PAB, Herschlag D, Lipfert J, Mathew RS, Shi X. Recording and Analyzing Nucleic Acid Distance Distributions with X-Ray Scattering Interferometry (XSI). Current Protocols in Nucleic Acid Chemistry. 73: e54. PMID 29927110 DOI: 10.1002/cpnc.54  1
2018 Gracia B, Al-Hashimi HM, Bisaria N, Das R, Herschlag D, Russell R. Hidden Structural Modules in a Cooperative RNA Folding Transition. Cell Reports. 22: 3240-3250. PMID 29562180 DOI: 10.1016/j.celrep.2018.02.101  1
2017 Moretti R, Lyskov S, Das R, Meiler J, Gray JJ. Web-accessible molecular modeling with Rosetta: The Rosetta Online Server That Includes Everyone (ROSIE). Protein Science : a Publication of the Protein Society. PMID 28960691 DOI: 10.1002/pro.3313  0.8
2017 Cheng CY, Kladwang W, Yesselman JD, Das R. RNA structure inference through chemical mapping after accidental or intentional mutations. Proceedings of the National Academy of Sciences of the United States of America. PMID 28851837 DOI: 10.1073/pnas.1619897114  0.6
2017 Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, ... Das R, et al. The Rosetta all-atom energy function for macromolecular modeling and design. Journal of Chemical Theory and Computation. PMID 28430426 DOI: 10.1021/acs.jctc.7b00125  1
2017 Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki J, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Feng D, et al. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. Rna (New York, N.Y.). PMID 28138060 DOI: 10.1261/rna.060368.116  0.6
2017 Parks JW, Kappel K, Das R, Stone MD. Single-molecule FRET-Rosetta reveals RNA structural rearrangements during human telomerase catalysis. Rna (New York, N.Y.). 23: 175-188. PMID 28096444 DOI: 10.1261/rna.058743.116  0.44
2016 Yesselman JD, Das R. Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server. Methods in Molecular Biology (Clifton, N.J.). 1490: 187-198. PMID 27665600 DOI: 10.1007/978-1-4939-6433-8_12  0.6
2016 Chou FC, Kladwang W, Kappel K, Das R. Blind tests of RNA nearest-neighbor energy prediction. Proceedings of the National Academy of Sciences of the United States of America. PMID 27402765 DOI: 10.1073/pnas.1523335113  0.56
2016 Anderson-Lee J, Fisker E, Kosaraju V, Wu M, Kong J, Lee J, Lee M, Zada M, Treuille A, Das R. Principles for Predicting RNA Secondary Structure Design Difficulty. Journal of Molecular Biology. PMID 26902426 DOI: 10.1016/j.jmb.2015.11.013  1
2016 Chou FC, Echols N, Terwilliger TC, Das R. RNA Structure Refinement Using the ERRASER-Phenix Pipeline. Methods in Molecular Biology (Clifton, N.J.). 1320: 269-82. PMID 26227049 DOI: 10.1007/978-1-4939-2763-0_17  0.56
2016 Das R, Karna S, Lai YC, Chou FC. Self-Adjusted Traveling Solvent Floating Zone Growth of Single Crystal CaFe2O4 Crystal Growth and Design. 16: 499-503. DOI: 10.1021/acs.cgd.5b01529  0.56
2016 Chou FC, Echols N, Terwilliger TC, Das R. RNA structure refi nement using the erraser-phenix pipeline Methods in Molecular Biology. 1320: 269-282. DOI: 10.1007/978-1-4939-2763-0_17  1
2015 Cordero P, Das R. Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis. Plos Computational Biology. 11: e1004473. PMID 26566145 DOI: 10.1371/journal.pcbi.1004473  1
2015 Yu Cheng C, Chou FC, Kladwang W, Tian S, Cordero P, Das R. Correction: Consistent global structures of complex RNA states through multidimensional chemical mapping. Elife. 4. PMID 26196348 DOI: 10.7554/eLife.10095  0.56
2015 Cheng CY, Chou FC, Kladwang W, Tian S, Cordero P, Das R. Consistent global structures of complex RNA states through multidimensional chemical mapping. Elife. 4: e07600. PMID 26035425 DOI: 10.7554/eLife.07600  0.56
2015 Tian S, Yesselman JD, Cordero P, Das R. Primerize: automated primer assembly for transcribing non-coding RNA domains. Nucleic Acids Research. 43: W522-6. PMID 25999345 DOI: 10.1093/nar/gkv538  0.6
2015 Yesselman JD, Das R. RNA-Redesign: a web server for fixed-backbone 3D design of RNA. Nucleic Acids Research. 43: W498-501. PMID 25964298 DOI: 10.1093/nar/gkv465  0.6
2015 Lee S, Kim H, Tian S, Lee T, Yoon S, Das R. Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles. Bioinformatics (Oxford, England). 31: 2808-15. PMID 25943472 DOI: 10.1093/bioinformatics/btv282  1
2015 Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferré-D'Amaré AR, Das R, Ding F, Dokholyan NV, et al. RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. Rna (New York, N.Y.). 21: 1066-84. PMID 25883046 DOI: 10.1261/rna.049502.114  0.56
2015 Cheng CY, Chou FC, Das R. Modeling complex RNA tertiary folds with Rosetta. Methods in Enzymology. 553: 35-64. PMID 25726460 DOI: 10.1016/bs.mie.2014.10.051  1
2015 Xue S, Tian S, Fujii K, Kladwang W, Das R, Barna M. RNA regulons in Hox 5' UTRs confer ribosome specificity to gene regulation. Nature. 517: 33-8. PMID 25409156 DOI: 10.1038/nature14010  1
2015 Cheng CY, Chou FC, Kladwang W, Tian S, Cordero P, Das R. Consistent global structures of complex RNA states through multidimensional chemical mapping Elife. 4. DOI: 10.7554/eLife.07600  1
2014 Lipfert J, Skinner GM, Keegstra JM, Hensgens T, Jager T, Dulin D, Köber M, Yu Z, Donkers SP, Chou FC, Das R, Dekker NH. Double-stranded RNA under force and torque: similarities to and striking differences from double-stranded DNA. Proceedings of the National Academy of Sciences of the United States of America. 111: 15408-13. PMID 25313077 DOI: 10.1073/pnas.1407197111  1
2014 Treuille A, Das R. Scientific rigor through videogames. Trends in Biochemical Sciences. 39: 507-9. PMID 25300714 DOI: 10.1016/j.tibs.2014.08.005  1
2014 Tian S, Cordero P, Kladwang W, Das R. High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states. Rna (New York, N.Y.). 20: 1815-26. PMID 25183835 DOI: 10.1261/rna.044321.114  1
2014 Chou FC, Lipfert J, Das R. Blind predictions of DNA and RNA tweezers experiments with force and torque Plos Computational Biology. 10: e1003756. PMID 25102226 DOI: 10.1371/journal.pcbi.1003756  1
2014 Kladwang W, Mann TH, Becka A, Tian S, Kim H, Yoon S, Das R. Standardization of RNA chemical mapping experiments. Biochemistry. 53: 3063-5. PMID 24766159 DOI: 10.1021/bi5003426  1
2014 Beauchamp KA, Pande VS, Das R. Bayesian energy landscape tilting: Towards concordant models of molecular ensembles Biophysical Journal. 106: 1381-1390. PMID 24655513 DOI: 10.1016/j.bpj.2014.02.009  1
2014 Lipfert J, Doniach S, Das R, Herschlag D. Understanding nucleic acid-ion interactions. Annual Review of Biochemistry. 83: 813-41. PMID 24606136 DOI: 10.1146/annurev-biochem-060409-092720  1
2014 Sripakdeevong P, Cevec M, Chang AT, Erat MC, Ziegeler M, Zhao Q, Fox GE, Gao X, Kennedy SD, Kierzek R, Nikonowicz EP, Schwalbe H, Sigel RK, Turner DH, Das R. Structure determination of noncanonical RNA motifs guided by ¹H NMR chemical shifts. Nature Methods. 11: 413-6. PMID 24584194 DOI: 10.1038/nmeth.2876  1
2014 Lee J, Kladwang W, Lee M, Cantu D, Azizyan M, Kim H, Limpaecher A, Yoon S, Treuille A, Das R. RNA design rules from a massive open laboratory. Proceedings of the National Academy of Sciences of the United States of America. 111: 2122-7. PMID 24469816 DOI: 10.1073/pnas.1313039111  1
2014 Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg O, Lorimer D, Luecke H, et al. Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Proteins. 82: 26-42. PMID 24318984 DOI: 10.1002/prot.24489  1
2014 Seetin MG, Kladwang W, Bida JP, Das R. Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol. Methods in Molecular Biology (Clifton, N.J.). 1086: 95-117. PMID 24136600 DOI: 10.1007/978-1-62703-667-2_6  1
2014 Cordero P, Kladwang W, VanLang CC, Das R. The mutate-and-map protocol for inferring base pairs in structured RNA. Methods in Molecular Biology (Clifton, N.J.). 1086: 53-77. PMID 24136598 DOI: 10.1007/978-1-62703-667-2_4  1
2013 Das R. Atomic-accuracy prediction of protein loop structures through an RNA-inspired Ansatz. Plos One. 8: e74830. PMID 24204571 DOI: 10.1371/journal.pone.0074830  1
2013 Drew K, Renfrew PD, Craven TW, Butterfoss GL, Chou FC, Lyskov S, Bullock BN, Watkins A, Labonte JW, Pacella M, Kilambi KP, Leaver-Fay A, Kuhlman B, Gray JJ, Bradley P, ... ... Das R, et al. Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design. Plos One. 8: e67051. PMID 23869206 DOI: 10.1371/journal.pone.0067051  1
2013 Kim H, Cordero P, Das R, Yoon S. HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis. Nucleic Acids Research. 41: W492-8. PMID 23761448 DOI: 10.1093/nar/gkt501  1
2013 Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, ... ... Das R, et al. Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). Plos One. 8: e63906. PMID 23717507 DOI: 10.1371/journal.pone.0063906  1
2013 Adams PD, Baker D, Brunger AT, Das R, DiMaio F, Read RJ, Richardson DC, Richardson JS, Terwilliger TC. Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. Annual Review of Biophysics. 42: 265-87. PMID 23451892 DOI: 10.1146/annurev-biophys-083012-130253  1
2013 Chou FC, Sripakdeevong P, Dibrov SM, Hermann T, Das R. Correcting pervasive errors in RNA crystallography through enumerative structure prediction. Nature Methods. 10: 74-6. PMID 23202432 DOI: 10.1038/nmeth.2262  1
2013 Molski MA, Goodman JL, Chou FC, Baker D, Das R, Schepartz A. Remodeling a β-peptide bundle Chemical Science. 4: 319-324. DOI: 10.1039/c2sc21117c  1
2012 Cordero P, Lucks JB, Das R. An RNA Mapping DataBase for curating RNA structure mapping experiments. Bioinformatics (Oxford, England). 28: 3006-8. PMID 22976082 DOI: 10.1093/bioinformatics/bts554  1
2012 Cordero P, Kladwang W, VanLang CC, Das R. Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference. Biochemistry. 51: 7037-9. PMID 22913637 DOI: 10.1021/bi3008802  1
2012 Kladwang W, Hum J, Das R. Ultraviolet shadowing of RNA can cause significant chemical damage in seconds. Scientific Reports. 2: 517. PMID 22816040 DOI: 10.1038/srep00517  1
2012 Frederiksen JK, Li NS, Das R, Herschlag D, Piccirilli JA. Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding. Rna (New York, N.Y.). 18: 1123-41. PMID 22539523 DOI: 10.1261/rna.028738.111  1
2012 Cruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S, Das R, Ding F, Dokholyan NV, Flores SC, Huang L, Lavender CA, Lisi V, Major F, Mikolajczak K, et al. RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. Rna (New York, N.Y.). 18: 610-25. PMID 22361291 DOI: 10.1261/rna.031054.111  1
2012 Kladwang W, Chou FC, Das R. Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches. Journal of the American Chemical Society. 134: 1404-7. PMID 22192063 DOI: 10.1021/ja2093508  1
2012 Beauchamp KA, Lin YS, Das R, Pande VS. Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements Journal of Chemical Theory and Computation. 8: 1409-1414. DOI: 10.1021/ct2007814  1
2011 Sripakdeevong P, Kladwang W, Das R. An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling. Proceedings of the National Academy of Sciences of the United States of America. 108: 20573-8. PMID 22143768 DOI: 10.1073/pnas.1106516108  1
2011 Kladwang W, VanLang CC, Cordero P, Das R. A two-dimensional mutate-and-map strategy for non-coding RNA structure. Nature Chemistry. 3: 954-62. PMID 22109276 DOI: 10.1038/nchem.1176  1
2011 Kladwang W, VanLang CC, Cordero P, Das R. Understanding the errors of SHAPE-directed RNA structure modeling. Biochemistry. 50: 8049-56. PMID 21842868 DOI: 10.1021/bi200524n  1
2011 Beauchamp KA, Ensign DL, Das R, Pande VS. Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments Proceedings of the National Academy of Sciences of the United States of America. 108: 12734-12739. PMID 21768345 DOI: 10.1073/pnas.1010880108  1
2011 Das R. Four small puzzles that Rosetta doesn't solve. Plos One. 6: e20044. PMID 21625446 DOI: 10.1371/journal.pone.0020044  1
2011 Rocca-Serra P, Bellaousov S, Birmingham A, Chen C, Cordero P, Das R, Davis-Neulander L, Duncan CD, Halvorsen M, Knight R, Leontis NB, Mathews DH, Ritz J, Stombaugh J, Weeks KM, et al. Sharing and archiving nucleic acid structure mapping data. Rna (New York, N.Y.). 17: 1204-12. PMID 21610212 DOI: 10.1261/rna.2753211  1
2011 Yoon S, Kim J, Hum J, Kim H, Park S, Kladwang W, Das R. HiTRACE: high-throughput robust analysis for capillary electrophoresis. Bioinformatics (Oxford, England). 27: 1798-805. PMID 21561922 DOI: 10.1093/bioinformatics/btr277  1
2011 Kladwang W, Cordero P, Das R. A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA. Rna (New York, N.Y.). 17: 522-34. PMID 21239468 DOI: 10.1261/rna.2516311  1
2011 Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, ... ... Das R, et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods in Enzymology. 487: 545-74. PMID 21187238 DOI: 10.1016/B978-0-12-381270-4.00019-6  1
2010 Kladwang W, Das R. 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. PMID 20677780 DOI: 10.1021/bi101123g  1
2010 Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, Thompson J, Havranek JJ, Das R, Bradley P, Baker D. Rosetta in CAPRI rounds 13-19. Proteins. 78: 3212-8. PMID 20597089 DOI: 10.1002/prot.22784  1
2010 Das R, Karanicolas J, Baker D. Atomic accuracy in predicting and designing noncanonical RNA structure. Nature Methods. 7: 291-4. PMID 20190761 DOI: 10.1038/nmeth.1433  1
2009 Das R, André I, Shen Y, Wu Y, Lemak A, Bansal S, Arrowsmith CH, Szyperski T, Baker D. Simultaneous prediction of protein folding and docking at high resolution. Proceedings of the National Academy of Sciences of the United States of America. 106: 18978-83. PMID 19864631 DOI: 10.1073/pnas.0904407106  1
2009 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 BH, Das R, Grishin NV, et al. Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins. 77: 89-99. PMID 19701941 DOI: 10.1002/prot.22540  1
2009 Kim J, Yu S, Shim B, Kim H, Min H, Chung EY, Das R, Yoon S. A robust peak detection method for RNA structure inference by high-throughput contact mapping. Bioinformatics (Oxford, England). 25: 1137-44. PMID 19246511 DOI: 10.1093/bioinformatics/btp110  1
2009 Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, et al. Outcome of a workshop on applications of protein models in biomedical research. Structure (London, England : 1993). 17: 151-9. PMID 19217386 DOI: 10.1016/j.str.2008.12.014  1
2009 Das R, Baker D. Prospects for de novo phasing with de novo protein models. Acta Crystallographica. Section D, Biological Crystallography. 65: 169-75. PMID 19171972 DOI: 10.1107/S0907444908020039  1
2009 Jonikas MA, Radmer RJ, Laederach A, Das R, Pearlman S, Herschlag D, Altman RB. Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. Rna (New York, N.Y.). 15: 189-99. PMID 19144906 DOI: 10.1261/rna.1270809  1
2009 Mathew-Fenn RS, Das R, Fenn TD, Schneiders M, Harbury PAB. Response to comment on "remeasuring the double helix" Science. 325: 538-c. DOI: 10.1126/science.1168876  1
2009 Blum B, Jordan MI, Kim DE, Das R, Bradley P, Baker D. Feature selection methods for improving protein structure prediction with Rosetta Advances in Neural Information Processing Systems 20 - Proceedings of the 2007 Conference 1
2008 Mathew-Fenn RS, Das R, Silverman JA, Walker PA, Harbury PA. A molecular ruler for measuring quantitative distance distributions. Plos One. 3: e3229. PMID 18927606 DOI: 10.1371/journal.pone.0003229  1
2008 Mathew-Fenn RS, Das R, Harbury PA. Remeasuring the double helix. Science (New York, N.Y.). 322: 446-9. PMID 18927394 DOI: 10.1126/science.1158881  1
2008 Laederach A, Das R, Vicens Q, Pearlman SM, Brenowitz M, Herschlag D, Altman RB. Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Nature Protocols. 3: 1395-401. PMID 18772866 DOI: 10.1038/nprot.2008.134  1
2008 Das R, Baker D. Macromolecular modeling with rosetta. Annual Review of Biochemistry. 77: 363-82. PMID 18410248 DOI: 10.1146/annurev.biochem.77.062906.171838  1
2008 Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans JP, Baker D, Piccirilli JA, Altman RB, Herschlag D. Structural inference of native and partially folded RNA by high-throughput contact mapping. Proceedings of the National Academy of Sciences of the United States of America. 105: 4144-9. PMID 18322008 DOI: 10.1073/pnas.0709032105  1
2007 Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D. High-resolution structure prediction and the crystallographic phase problem. Nature. 450: 259-64. PMID 17934447 DOI: 10.1038/nature06249  1
2007 Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmström L, Wollacott AM, Wang C, et al. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins. 69: 118-28. PMID 17894356 DOI: 10.1002/prot.21636  1
2007 Das R, Baker D. Automated de novo prediction of native-like RNA tertiary structures. Proceedings of the National Academy of Sciences of the United States of America. 104: 14664-9. PMID 17726102 DOI: 10.1073/pnas.0703836104  1
2007 Lipfert J, Das R, Chu VB, Kudaravalli M, Boyd N, Herschlag D, Doniach S. Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. Journal of Molecular Biology. 365: 1393-406. PMID 17118400 DOI: 10.1016/j.jmb.2006.10.022  1
2006 Russell R, Das R, Suh H, Travers KJ, Laederach A, Engelhardt MA, Herschlag D. The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. Journal of Molecular Biology. 363: 531-44. PMID 16963081 DOI: 10.1016/j.jmb.2006.08.024  1
2005 Das R, Travers KJ, Bai Y, Herschlag D. Determining the Mg2+ stoichiometry for folding an RNA metal ion core. Journal of the American Chemical Society. 127: 8272-3. PMID 15941246 DOI: 10.1021/ja051422h  1
2005 Das R, Laederach A, Pearlman SM, Herschlag D, Altman RB. SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. Rna (New York, N.Y.). 11: 344-54. PMID 15701734 DOI: 10.1261/rna.7214405  1
2005 Bai Y, Das R, Millett IS, Herschlag D, Doniach S. Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution. Proceedings of the National Academy of Sciences of the United States of America. 102: 1035-40. PMID 15647360 DOI: 10.1073/pnas.0404448102  1
2004 Andresen K, Das R, Park HY, Smith H, Kwok LW, Lamb JS, Kirkland EJ, Herschlag D, Finkelstein KD, Pollack L. Spatial distribution of competing ions around DNA in solution. Physical Review Letters. 93: 248103. PMID 15697865 DOI: 10.1103/PhysRevLett.93.248103  1
2004 Takamoto K, Das R, He Q, Doniach S, Brenowitz M, Herschlag D, Chance MR. 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. PMID 15491606 DOI: 10.1016/j.jmb.2004.08.080  1
2003 Das R, Kwok LW, Millett IS, Bai Y, Mills TT, Jacob J, Maskel GS, Seifert S, Mochrie SG, Thiyagarajan P, Doniach S, Pollack L, Herschlag D. The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme. Journal of Molecular Biology. 332: 311-9. PMID 12948483 DOI: 10.1016/S0022-2836(03)00854-4  1
2003 Das R, Mills TT, Kwok LW, Maskel GS, Millett IS, Doniach S, Finkelstein KD, Herschlag D, Pollack L. Counterion distribution around DNA probed by solution X-ray scattering. Physical Review Letters. 90: 188103. PMID 12786045  1
2003 Bartley LE, Zhuang X, Das R, Chu S, Herschlag D. Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA. Journal of Molecular Biology. 328: 1011-26. PMID 12729738 DOI: 10.1016/S0022-2836(03)00272-9  1
2003 Saunders R, Kneissl R, Grainge K, Grainger WF, Jones ME, Maggi A, Das R, Edge AC, Lasenby AN, Pooley GG, Miyoshi SJ, Tsuruta T, Yamashita K, Tawara Y, Furuzawa A, et al. A measurement of H0 from Ryle Telescope, ASCA and ROSAT observations of Abell 773 Monthly Notices of the Royal Astronomical Society. 341: 937-940. DOI: 10.1046/j.1365-8711.2003.06467.x  1
2002 Grainger WF, Das R, Grainge K, Jones ME, Kneissl R, Pooley GG, Saunders RDE. 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. DOI: 10.1046/j.1365-8711.2002.05815.x  1
2002 Cotter G, Buttery HJ, Das R, Jones ME, Grainge K, Pooley GG, Saunders R. 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. DOI: 10.1046/j.1365-8711.2002.05262.x  1
2002 Cotter G, Buttery HJ, Rawlings S, Croft S, Hill GJ, Gay P, Das R, Drory N, Grainge K, Grainger WF, Jones ME, Pooley GG, Saunders R. Detection of a cosmic microwave background decrement towards a cluster of mJy radio sources Monthly Notices of the Royal Astronomical Society. 331: 1-6. DOI: 10.1046/j.1365-8711.2002.04996.x  1
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