Rhiju Das

Overview

Best Publications

• ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.

  Andrew Leaver-Fay;Michael Tyka;Steven M. Lewis;Oliver F. Lange

  2124
  Citations

• The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.

  Rebecca F. Alford;Andrew Leaver-Fay;Jeliazko R. Jeliazkov;Matthew J. O’Meara

  1306
  Citations

• Macromolecular Modeling with Rosetta

  Rhiju Das;David Baker

  1085
  Citations

• Macromolecular modeling and design in Rosetta: recent methods and frameworks

  Julia Koehler Leman;Brian D. Weitzner;Brian D. Weitzner;Steven M. Lewis;Steven M. Lewis;Jared Adolf-Bryfogle

  847
  Citations

• Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

  Kathrin Leppek;Rhiju Das;Maria Barna

  756
  Citations

• Structure prediction for CASP8 with all‐atom refinement using Rosetta

  Srivatsan Raman;Robert Vernon;James Thompson;Michael Tyka

  561
  Citations

• Automated de novo prediction of native-like RNA tertiary structures

  Rhiju Das;David Baker

  523
  Citations

• Understanding Nucleic Acid–Ion Interactions

  Jan Lipfert;Sebastian Doniach;Rhiju Das;Daniel Herschlag

  519
  Citations

• Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements.

  Kyle A. Beauchamp;Yu-Shan Lin;Rhiju Das;Vijay S. Pande

  457
  Citations

• Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE).

  Sergey Lyskov;Fang Chieh Chou;Shane Ó Conchúir;Bryan S. Der

  432
  Citations

• Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties.

  Steven Boeynaems;Alex S. Holehouse;Venera Weinhardt;Venera Weinhardt;Denes Kovacs

  432
  Citations

• Atomic accuracy in predicting and designing noncanonical RNA structure

  Rhiju Das;John Karanicolas;J. David Baker

  407
  Citations

• SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments

  Rhiju Das;Alain Laederach;Samuel M. Pearlman;Daniel Herschlag

  401
  Citations

• High-resolution structure prediction and the crystallographic phase problem

  Bin Qian;Srivatsan Raman;Rhiju Das;Philip Bradley

  381
  Citations

• Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

  Magdalena A. Jonikas;Randall J. Radmer;Alain Laederach;Rhiju Das

  379
  Citations

• RNA design rules from a massive open laboratory

  Jeehyung Lee;Wipapat Kladwang;Minjae Lee;Daniel Cantu

  361
  Citations

• RNA regulons in Hox 5′ UTRs confer ribosome specificity to gene regulation

  Shifeng Xue;Siqi Tian;Kotaro Fujii;Wipapat Kladwang

  312
  Citations

• RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

  José Almeida Cruz;Marc Frédérick Blanchet;Michal Boniecki;Janusz M. Bujnicki;Janusz M. Bujnicki

  293
  Citations

• Geometric deep learning of RNA structure.

  Raphael J. L. Townshend;Stephan Eismann;Andrew M. Watkins;Ramya Rangan

  286
  Citations

• Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.

  Rhiju Das;Bin Qian;Srivatsan Raman;Robert Vernon

  274
  Citations