Rhiju Das
Rhiju Das
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ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules
A Leaver-Fay, M Tyka, SM Lewis, OF Lange, J Thompson, R Jacak, ...
Methods in enzymology 487, 545-574, 2011
The Rosetta all-atom energy function for macromolecular modeling and design
RF Alford, A Leaver-Fay, JR Jeliazkov, MJ O’Meara, FP DiMaio, H Park, ...
Journal of chemical theory and computation 13 (6), 3031-3048, 2017
Macromolecular modeling with rosetta
R Das, D Baker
Annu. Rev. Biochem. 77 (1), 363-382, 2008
Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them
K Leppek, R Das, M Barna
Nature reviews Molecular cell biology 19 (3), 158-174, 2018
Macromolecular modeling and design in Rosetta: recent methods and frameworks
JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle, N Alam, RF Alford, ...
Nature methods 17 (7), 665-680, 2020
Structure prediction for CASP8 with all‐atom refinement using Rosetta
S Raman, R Vernon, J Thompson, M Tyka, R Sadreyev, J Pei, D Kim, ...
Proteins: Structure, Function, and Bioinformatics 77 (S9), 89-99, 2009
Automated de novo prediction of native-like RNA tertiary structures
R Das, D Baker
Proceedings of the National Academy of Sciences 104 (37), 14664-14669, 2007
Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements
KA Beauchamp, YS Lin, R Das, VS Pande
Journal of chemical theory and computation 8 (4), 1409-1414, 2012
Understanding nucleic acid–ion interactions
J Lipfert, S Doniach, R Das, D Herschlag
Annual review of biochemistry 83 (1), 813-841, 2014
Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE)
S Lyskov, FC Chou, SO Conchuir, BS Der, K Drew, D Kuroda, J Xu, ...
PloS one 8 (5), e63906, 2013
Atomic accuracy in predicting and designing noncanonical RNA structure
R Das, J Karanicolas, D Baker
Nature methods 7 (4), 291-294, 2010
High-resolution structure prediction and the crystallographic phase problem
B Qian, S Raman, R Das, P Bradley, AJ McCoy, RJ Read, D Baker
Nature 450 (7167), 259-264, 2007
SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments
R Das, A Laederach, SM Pearlman, D Herschlag, RB Altman
Rna 11 (3), 344-354, 2005
Spontaneous driving forces give rise to protein− RNA condensates with coexisting phases and complex material properties
S Boeynaems, AS Holehouse, V Weinhardt, D Kovacs, J Van Lindt, ...
Proceedings of the National Academy of Sciences 116 (16), 7889-7898, 2019
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters
MA Jonikas, RJ Radmer, A Laederach, R Das, S Pearlman, D Herschlag, ...
Rna 15 (2), 189-199, 2009
RNA design rules from a massive open laboratory
J Lee, W Kladwang, M Lee, D Cantu, M Azizyan, H Kim, A Limpaecher, ...
Proceedings of the National Academy of Sciences 111 (6), 2122-2127, 2014
RNA regulons in Hox 5′ UTRs confer ribosome specificity to gene regulation
S Xue, S Tian, K Fujii, W Kladwang, R Das, M Barna
Nature 517 (7532), 33-38, 2015
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction
JA Cruz, MF Blanchet, M Boniecki, JM Bujnicki, SJ Chen, S Cao, R Das, ...
Rna 18 (4), 610-625, 2012
Structure prediction for CASP7 targets using extensive all‐atom refinement with Rosetta@ home
R Das, B Qian, S Raman, R Vernon, J Thompson, P Bradley, S Khare, ...
Proteins: Structure, Function, and Bioinformatics 69 (S8), 118-128, 2007
Geometric deep learning of RNA structure
RJL Townshend, S Eismann, AM Watkins, R Rangan, M Karelina, R Das, ...
Science 373 (6558), 1047-1051, 2021
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