Rhiju Das

发表

High-resolution structure prediction and the crystallographic phase problem

P. Bradley, D. Baker, B. Qian, 2007, Nature.

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

Rhiju Das, Shifeng Xue, Siqi Tian, 2014, Nature.

Scientific rigor through videogames.

Adrien Treuille, Rhiju Das, 2014, Trends in biochemical sciences.

RNA design rules from a massive open laboratory

Minjae Lee, Sungroh Yoon, Adrien Treuille, 2014, Proceedings of the National Academy of Sciences.

Atomic accuracy in predicting and designing non-canonical RNA structure

D. Baker, J. Karanicolas, Rhiju Das, 2010, Nature Methods.

Structural inference of native and partially folded RNA by high-throughput contact mapping

Magdalena A. Jonikas, D. Baker, R. Altman, 2008, Proceedings of the National Academy of Sciences.

The mutate-and-map protocol for inferring base pairs in structured RNA.

Rhiju Das, W. Kladwang, P. Cordero, 2013, Methods in molecular biology.

A two-dimensional mutate-and-map strategy for non-coding RNA structure.

Rhiju Das, W. Kladwang, P. Cordero, 2011, Nature chemistry.

The paradoxical behavior of a highly structured misfolded intermediate in RNA folding.

D. Herschlag, Rhiju Das, A. Laederach, 2006, Journal of molecular biology.

Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding.

D. Herschlag, Rhiju Das, J. Piccirilli, 2012, RNA.

Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference.

Rhiju Das, W. Kladwang, P. Cordero, 2012, Biochemistry.

Understanding the errors of SHAPE-directed RNA structure modeling.

Rhiju Das, W. Kladwang, P. Cordero, 2011, Biochemistry.

The Rosetta all-atom energy function for macromolecular modeling and design

Roland L. Dunbrack, Jason W. Labonte, Jeffrey J. Gray, 2017, bioRxiv.

Feature Selection Methods for Improving Protein Structure Prediction with Rosetta

David Kim, Michael I. Jordan, David Baker, 2007, NIPS.

Principles for Predicting RNA Secondary Structure Design Difficulty.

Michelle J. Wu, Adrien Treuille, Jeehyung Lee, 2016, Journal of molecular biology.

Structure prediction for CASP8 with all‐atom refinement using Rosetta

Oliver F. Lange, David Kim, Nick V Grishin, 2009, Proteins.

Correcting a SHAPE-directed RNA structure by a mutate-map-rescue approach

Pablo Cordero, Siqi Tian, Rhiju Das, 2014, bioRxiv.

A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA.

Rhiju Das, W. Kladwang, P. Cordero, 2011, RNA.

A mutate-and-map strategy for inferring base pairs in structured nucleic acids: proof of concept on a DNA/RNA helix.

Rhiju Das, W. Kladwang, 2010, Biochemistry.

Bayesian Energy Landscape Tilting: Towards Concordant Models of Molecular Ensembles

Rhiju Das, Vijay S Pande, Kyle A Beauchamp, 2014, bioRxiv.

RNA 3D modeling with FARFAR2, online

Rhiju Das, Andrew Watkins, Rhiju Das, 2020, bioRxiv.

Consistent global structures of complex RNA states through multidimensional chemical mapping

Rhiju Das, Siqi Tian, W. Kladwang, 2015, eLife.

Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)

Brian D. Weitzner, Jeffrey J. Gray, Bryan S. Der, 2013, PloS one.

Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts

D. Turner, R. Kierzek, H. Schwalbe, 2014, Nature Methods.

FARFAR2: Improved De Novo Rosetta Prediction of Complex Global RNA Folds.

Rhiju Das, A. Watkins, R. Rangan, 2020, Structure.

The Rosetta all-atom energy function for macromolecular modeling and design

Roland L. Dunbrack, Richard Bonneau, P. Douglas Renfrew, 2017, bioRxiv.

Automated de novo prediction of native-like RNA tertiary structures

D. Baker, Rhiju Das, D. Baker, 2007, Proceedings of the National Academy of Sciences.

Blind tests of RNA nearest-neighbor energy prediction

Rhiju Das, W. Kladwang, K. Kappel, 2016, Proceedings of the National Academy of Sciences.

An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling

Rhiju Das, W. Kladwang, Parin Sripakdeevong, 2011, Proceedings of the National Academy of Sciences.

Scientific Discovery Games for Biomedical Research.

Ingmar H. Riedel-Kruse, Rhiju Das, Peter Washington, 2019, Annual review of biomedical data science.

EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogame

Rhiju Das, Fernando Portela, Rohan V. Koodli, 2019, PLoS Comput. Biol..

Blind prediction of noncanonical RNA structure at atomic accuracy

Luc Jaeger, Rhiju Das, Wipapat Kladwang, 2017, Science Advances.

Standardization of RNA Chemical Mapping Experiments

Rhiju Das, Sungroh Yoon, Siqi Tian, 2014, Biochemistry.

Modeling complex RNA tertiary folds with Rosetta.

Rhiju Das, C. Cheng, Fang-Chieh Chou, 2015, Methods in enzymology.

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.

Katarzyna J Purzycka, K. Weeks, Zhichao Miao, 2017, RNA.

Blind prediction of noncanonical RNA structure at atomic accuracy

Rhiju Das, W. Kladwang, L. Jaeger, 2017, bioRxiv.

SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments.

R. Altman, D. Herschlag, Rhiju Das, 2005, RNA.

Response to Comment on “Remeasuring the Double Helix”

Rhiju Das, P. Harbury, Rebecca S. Mathew-Fenn, 2009, Science.

Understanding nucleic acid-ion interactions.

Sebastian Doniach, Daniel Herschlag, Rhiju Das, 2014, Annual review of biochemistry.

Allosteric mechanism of the V. vulnificus adenine riboswitch resolved by four-dimensional chemical mapping

Rhiju Das, Siqi Tian, W. Kladwang, 2018, eLife.

Allosteric Logic of the V. vulnificus Adenine Riboswitch Resolved by Four-dimensional Chemical Mapping

Rhiju Das, Siqi Tian, W. Kladwang, 2017, bioRxiv.

A quantitative and predictive model for RNA binding by human Pumilio proteins

Curtis J. Layton, Johan O. L. Andreasson, D. Herschlag, 2018, bioRxiv.

Cryo-electron Microscopy and Exploratory Antisense Targeting of the 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome

W. Chiu, Rhiju Das, W. Kladwang, 2020, bioRxiv.

Theoretical basis for stabilizing messenger RNA through secondary structure design

Christian A. Choe, Do Soon Kim, John J. Nicol, 2020, bioRxiv.

Prospects for recurrent neural network models to learn RNA biophysics from high-throughput data

Rhiju Das, Wipapat Kladwang, Michelle J. Wu, 2017, bioRxiv.

Geometric deep learning of RNA structure

Andrew M. Watkins, Ron O. Dror, Rhiju Das, 2021, Science.

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

R. Pappu, C. Larabell, Rhiju Das, 2018, Proceedings of the National Academy of Sciences.

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

Magdalena A. Jonikas, R. Altman, D. Herschlag, 2009, RNA.

Sharing and archiving nucleic acid structure mapping data.

Craig L. Zirbel, R. Knight, D. Mathews, 2011, RNA.

A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites

Rhiju Das, J. Piccirilli, A. Watkins, 2019, Nature Communications.

Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA.

X. Zhuang, D. Herschlag, S. Chu, 2003, Journal of molecular biology.

Simultaneous prediction of protein folding and docking at high resolution

D. Baker, I. André, Rhiju Das, 2009, Proceedings of the National Academy of Sciences.

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

Rhiju Das, Vijay S Pande, Kyle A Beauchamp, 2012, Journal of chemical theory and computation.

Quantitative comparison of villin headpiece subdomain simulations and triplet–triplet energy transfer experiments

Kyle A. Beauchamp, V. Pande, Rhiju Das, 2011, Proceedings of the National Academy of Sciences.

Computational design of three-dimensional RNA structure and function

Paul D. Carlson, Erik D. Carlson, Alexandra N. Ooms, 2019, Nature Nanotechnology.

Double-stranded RNA under force and torque: Similarities to and striking differences from double-stranded DNA

Rhiju Das, Fang-Chieh Chou, J. Lipfert, 2014, Proceedings of the National Academy of Sciences.

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

Rhiju Das, Maria Barna, Rhiju Das, 2017, Nature Reviews Molecular Cell Biology.

RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction.

Feng Ding, Kristian Rother, Thomas Hermann, 2012, RNA.

A unified mechanism for intron and exon definition and back-splicing

Rhiju Das, Z. Zhou, K. Kappel, 2019, Nature.

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

Christopher A. Lavender, K. Weeks, E. Westhof, 2012 .

2 Theoretical Basis of Likelihood Methods in Molecular Phylogenetic Inference

Rhiju Das, 2000 .

A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins.

Daniel Herschlag, Rhiju Das, William J. Greenleaf, 2019, Molecular cell.

Automated Design of Diverse Stand-Alone Riboswitches

Rhiju Das, Wipapat Kladwang, Michelle J. Wu, 2019, ACS synthetic biology.

Functional and structural basis of extreme non-coding conservation in vertebrate 5’UTRs

Hua Tang, Rhiju Das, M. Barna, 2020 .

Controllable molecular motors engineered from myosin and RNA

Paul V. Ruijgrok, Rhiju Das, C. Cheng, 2017, Nature Nanotechnology.

Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular switches

Michelle J. Wu, Michael R. Gotrik, Johan O. L. Andreasson, 2022, Proceedings of the National Academy of Sciences of the United States of America.

Recording and Analyzing Nucleic Acid Distance Distributions with X‐Ray Scattering Interferometry (XSI)

D. Herschlag, Rhiju Das, P. Harbury, 2018, Current protocols in nucleic acid chemistry.

RNA structure through multidimensional chemical mapping

Rhiju Das, Siqi Tian, 2016, bioRxiv.

Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation

D. Herschlag, Rhiju Das, W. Greenleaf, 2019, Proceedings of the National Academy of Sciences.

RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look

Rhiju Das, R. Rangan, I. N. Zheludev, 2020, RNA.

Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis

A. Kundaje, Rhiju Das, Jin Billy Li, 2019, Nature Communications.

Resource Sampling Native-like Struc tures of RNA-Protein Complexes through Rosetta Folding and Docking Graphical Abstract Highlights

Rhiju Das, K. Kappel, 2018 .

RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses

Rhiju Das, R. Rangan, I. N. Zheludev, 2020, bioRxiv.

Folding heterogeneity in the essential human telomerase RNA three-way junction.

Michael D. Stone, Rhiju Das, J. Hentschel, 2020, RNA.

Folding heterogeneity in the essential human telomerase RNA three-way junction

Michael D. Stone, Rhiju Das, J. Hentschel, 2019, bioRxiv.

RNA structure inference through chemical mapping after accidental 1 or intentional mutations 2 3 4

Rhiju Das, W. Kladwang, C. Cheng, 2017 .

Protein loop structures can be solved at atomic resolution with an enumerative ansatz

Rhiju Das, 2012 .

Ribosome-induced RNA conformational changes in a viral 3′-UTR sense and regulate translation levels

Rhiju Das, Siqi Tian, J. Kieft, 2018, Nature Communications.

Correction to ‘Theoretical basis for stabilizing messenger RNA through secondary structure design’

Christian A. Choe, Do Soon Kim, John J. Nicol, 2021, Nucleic acids research.

Advances, Interactions, and Future Developments in the CNS, Phenix, and Rosetta Structural Biology Software Systems Annual Review of Biophysics

Randy J. Read, Paul D. Adams, David Baker, 2012 .

An Activity Switch in Human Telomerase Based on RNA Conformation and Shaped by TCAB1

Howard Y. Chang, Pedro J. Batista, A. Venteicher, 2018, Cell.

RNA 3D structure prediction guided by independent folding of homologous sequences

Rhiju Das, J. Bujnicki, K. Kappel, 2019, BMC Bioinformatics.

RNA 3D structure prediction using multiple sequence alignment information

Rhiju Das, J. Bujnicki, K. Kappel, 2019 .

Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2

S. Schaffert, P. Khatri, Rhiju Das, 2022, Nature Medicine.

Computationally-guided design and selection of ribosomal active site mutants with high activity

Ashty S. Karim, Do Soon Kim, Rhiju Das, 2022, bioRxiv.

Topological crossing in the misfolded Tetrahymena ribozyme resolved by cryo-EM

Rhiju Das, K. Kappel, G. Pintilie, 2022, Proceedings of the National Academy of Sciences of the United States of America.

Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome

Rhiju Das, W. Kladwang, R. Baric, 2021, Nature Structural & Molecular Biology.

Quantitative DMS mapping for automated RNA secondary structure inference

Rhiju Das, W. Kladwang, P. Cordero, 2012, 1207.1312.

Modeling Small Non-canonical RNA Motifs with the Rosetta FARFAR Server

Rhiju Das, J. Yesselman, 2015, bioRxiv.

Deep learning models for predicting RNA degradation via dual crowdsourcing

Do Soon Kim, John J. Nicol, Rhiju Das, 2021, ArXiv.

Three-dimensional structure-guided evolution of a ribosome with tethered subunits

Do Soon Kim, Rhiju Das, V. Topkar, 2022, Nature Chemical Biology.

Community science designed ribosomes with beneficial phenotypes

Rhiju Das, Jeff Anderson-Lee, Eli Fisker, 2021, bioRxiv.

Remodeling a β-peptide bundle

David Baker, Rhiju Das, Fang-Chieh Chou, 2013 .

FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds

Andrew M. Watkins, Rhiju Das, Rhiju Das, 2019, bioRxiv.

De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes

Rhiju Das, Georgios Skiniotis, Kalli Kappel, 2018, Nature Methods.

Computationally-guided design and selection of high performing ribosomal active site mutants

Ashty S. Karim, Do Soon Kim, Rhiju Das, 2022, Nucleic acids research.

Computational Design of Asymmetric Three-dimensional RNA Structures and Machines

Daniel Herschlag, Rhiju Das, Xuesong Shi, 2017, bioRxiv.

Transcription polymerase–catalyzed emergence of novel RNA replicons

Sindy K. Y. Tang, Rhiju Das, A. Fire, 2020, Science.

How to Kinetically Dissect an RNA Machine

Rhiju Das, R. Russell, 2021, Biochemistry.

Functional and structural basis of extreme conservation in vertebrate 5’ untranslated regions

Hua Tang, Rhiju Das, M. Barna, 2021, Nature Genetics.

RiboDraw: semiautomated two-dimensional drawing of RNA tertiary structure diagrams

Rhiju Das, A. Watkins, 2021, NAR genomics and bioinformatics.

Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

Christian A. Choe, Do Soon Kim, John J. Nicol, 2021, bioRxiv.

RNA secondary structure packages evaluated and improved by high-throughput experiments

Rhiju Das, Wipapat Kladwang, Hannah K. Wayment-Steele, 2020, bioRxiv.

De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes

Rui Zhao, Rhiju Das, Kalli Kappel, 2018, Nature Methods.

Single-molecule FRET-Rosetta reveals RNA structural rearrangements during human telomerase catalysis

Michael D. Stone, Rhiju Das, K. Kappel, 2017, RNA.

MOHCA-seq: RNA 3D models from single multiplexed proximity-mapping experiments

Siqi Tian, Rhiju Das, Fang-Chieh Chou, 2014, bioRxiv.

High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding

Daniel Herschlag, Rhiju Das, William James Greenleaf, 2018, Cell.

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

Jens Meiler, Florian Richter, David Baker, 2011, Methods in enzymology.

Two-dimensional chemical mapping for non-coding RNAs

Rhiju Das, Wipapat Kladwang, Pablo Cordero, 2011, 1104.0979.

RNA structure landscape of S. cerevisiae introns

M. Ares, Rhiju Das, R. Rangan, 2023, bioRxiv.

Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque

Rhiju Das, Fang-Chieh Chou, Jan Lipfert, 2014, PLoS Comput. Biol..

Correcting pervasive errors in RNA crystallography through enumerative structure prediction

Rhiju Das, Fang-Chieh Chou, Parin Sripakdeevong, 2011, Nature Methods.

Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments

Daniel Herschlag, Russ B Altman, Rhiju Das, 2008, Nature Protocols.

Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems.

David Baker, Randy J Read, Frank DiMaio, 2013, Annual review of biophysics.

An Activity Switch in Human Telomerase Based on RNA Conformation and Shaped by TCAB 1 Graphical Abstract Highlights

Howard Y. Chang, Pedro J. Batista, A. Venteicher, 2018 .

Outcome of a workshop on applications of protein models in biomedical research.

Roland L Dunbrack, Roland L. Dunbrack, Andrej Sali, 2009, Structure.

Structure of human telomerase holoenzyme with bound telomeric DNA

Rhiju Das, R. Rangan, K. Collins, 2021, Nature.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Brian D. Weitzner, Lars Malmström, Karen R. Khar, 2020, Nature Methods.

Web‐accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE)

Jens Meiler, Sergey Lyskov, Jeffrey J. Gray, 2018, Protein science : a publication of the Protein Society.

RNA-Redesign: a web server for fixed-backbone 3D design of RNA

Rhiju Das, Joseph D. Yesselman, Rhiju Das, 2015, Nucleic Acids Res..

Remeasuring the Double Helix

Rhiju Das, Rhiju Das, P. Harbury, 2008, Science.

Blind tests of RNA nearest neighbor energy prediction

Rhiju Das, W. Kladwang, K. Kappel, 2016, bioRxiv.

Why Can’t We Predict RNA Structure At Atomic Resolution?

Rhiju Das, Parin Sripakdeevong, Kyle A. Beauchamp, 2011, 1103.3032.

RNA tertiary structure energetics predicted by an ensemble model of the RNA double helix

Daniel Herschlag, Rhiju Das, William J. Greenleaf, 2018, bioRxiv.

RNA structure through multidimensional chemical mapping

Siqi Tian, Rhiju Das, Rhiju Das, 2016, bioRxiv.

Automated design of highly diverse riboswitches

Rhiju Das, William J. Greenleaf, Wipapat Kladwang, 2019, bioRxiv.

Ribosolve: Rapid determination of three-dimensional RNA-only structures

Andrew M. Watkins, Wah Chiu, Kaiming Zhang, 2019, bioRxiv.

Blind tests of RNA–protein binding affinity prediction

Daniel Herschlag, Rhiju Das, William J. Greenleaf, 2019, Proceedings of the National Academy of Sciences.

Dynamics of Human Telomerase

Rhiju Das, J. Parks, Michael D Stone, 2018 .

An RNA Mapping DataBase for curating RNA structure mapping experiments

Julius B. Lucks, Pablo Cordero, Rhiju Das, 2012, Bioinform..

The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme.

Rhiju Das, S. Mochrie, I. Millett, 2003, Journal of molecular biology.

Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol.

Rhiju Das, Wipapat Kladwang, Matthew G Seetin, 2013, Methods in molecular biology.

Macromolecular modeling with rosetta.

David Baker, Rhiju Das, D. Baker, 2008, Annual review of biochemistry.

RNA structure inference through chemical mapping after accidental or intentional mutations

Rhiju Das, Wipapat Kladwang, Rhiju Das, 2017, Proceedings of the National Academy of Sciences.

Primerize‐2D: automated primer design for RNA multidimensional chemical mapping

Siqi Tian, Rhiju Das, Rhiju Das, 2017, Bioinform..

Theoretical basis for stabilizing messenger RNA through secondary structure design

Christian A. Choe, Do Soon Kim, John J. Nicol, 2021, Nucleic acids research.

Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

Christian A. Choe, Do Soon Kim, John J. Nicol, 2022, Nature Communications.

Anomalous reverse transcription through chemical modifications in polyadenosine stretches

Rhiju Das, Wipapat Kladwang, Rhiju Das, 2020, bioRxiv.

Quantitative high-throughput tests of ubiquitous RNA secondary structure prediction algorithms via RNA/protein binding

Daniel Herschlag, Rhiju Das, William J. Greenleaf, 2019, bioRxiv.

A Quantitative and Predict ive Model for RNA Binding by Human Pumilio Proteins Graphical

Johan O. L. Andreasson, D. Herschlag, Rhiju Das, 2019 .

Hidden Structural Modules in a Cooperative RNA Folding Transition

D. Herschlag, Rhiju Das, H. Al‐Hashimi, 2018, Cell reports.

Can biopolymer structures be sampled enumeratively? Atomic-accuracy RNA loop modeling by a stepwise ansatz

Rhiju Das, Parin Sripakdeevong, Wipapat Kladwang, 2011, 1104.5278.

Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution.

Sebastian Doniach, Daniel Herschlag, Rhiju Das, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae.

Sebastian Doniach, Daniel Herschlag, Rhiju Das, 2007, Journal of molecular biology.

Atomic-Accuracy Prediction of Protein Loop Structures through an RNA-Inspired Ansatz

Rhiju Das, Rhiju Das, 2012, PloS one.

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

Feng Ding, Janusz M Bujnicki, Lin Huang, 2020, RNA.

Four Small Puzzles That Rosetta Doesn't Solve

Rhiju Das, Rhiju Das, 2011, PloS one.

PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design.

Brian D. Weitzner, Roland L. Dunbrack, Sergey Lyskov, 2020, Biophysicist.

Structure prediction for CASP7 targets using extensive all‐atom refinement with Rosetta@home

Lars Malmström, David Baker, Dylan Chivian, 2007, Proteins.

A robust peak detection method for RNA structure inference by high-throughput contact mapping

Byonghyo Shim, Sungroh Yoon, Seunghak Yu, 2009, Bioinform..

Evaluating riboswitch optimality.

Rhiju Das, Michelle J. Wu, Michael R. Gotrik, 2019, Methods in enzymology.

Structure and ligand binding of the glutamine-II riboswitch

Lin Huang, Rhiju Das, Andrew M Watkins, 2019, Nucleic acids research.

Structural Studies of Proteins and Nucleic Acids in Solution Using Small Angle X-Ray Scattering (SAXS)

Rhiju Das, S. Doniach, 2008 .

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

Marco Biasini, Victor Seguritan, Forest Rohwer, 2014, Proteins.

Prospects for de novo phasing with de novo protein models

David Baker, Rhiju Das, D. Baker, 2009, Acta crystallographica. Section D, Biological crystallography.

A Molecular Ruler for Measuring Quantitative Distance Distributions

Rhiju Das, P. Harbury, Rebecca S. Mathew-Fenn, 2008, PloS one.

Redesigning the Eterna100 for the Vienna 2 folding engine

Rohan V. Koodli, Rhiju Das, H. Wayment-Steele, 2021, bioRxiv.

RNA design movesets and strategies from an Internet-scale videogame

Rhiju Das, Fernando Portela, Rohan V. Koodli, 2019 .

EternaBrain: Automated RNA design through move sets from an Internet-scale RNA videogame

Rhiju Das, Fernando Portela, Rohan V. Koodli, 2018, bioRxiv.

SentRNA: Improving computational RNA design by incorporating a prior of human design strategies pdf

Vijay S. Pande, Rhiju Das, Jade Shi, 2018, ArXiv.

Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution

W. Chiu, Rhiju Das, K. Kappel, 2019, Nature Communications.

Using Rosetta for RNA homology modeling.

Rhiju Das, Andrew M Watkins, Ramya Rangan, 2019, Methods in enzymology.

Author Correction: Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

Rhiju Das, M. Barna, Kathrin Leppek, 2018, Nature Reviews Molecular Cell Biology.

Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations.

Sebastian Doniach, Daniel Herschlag, Rhiju Das, 2004, Journal of molecular biology.

Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches.

Rhiju Das, Fang-Chieh Chou, Wipapat Kladwang, 2012, Journal of the American Chemical Society.

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

W. Chiu, Rhiju Das, W. Kladwang, 2020, Nature Methods.

Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design

Andrew Watkins, Krishna Praneeth Kilambi, P. Douglas Renfrew, 2013, PloS one.

Determining the Mg2+ stoichiometry for folding an RNA metal ion core.

D. Herschlag, Rhiju Das, K. Travers, 2005, Journal of the American Chemical Society.

Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis

Pablo Cordero, Rhiju Das, Rhiju Das, 2015, PLoS Comput. Biol..

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

Feng Ding, Jian Wang, Janusz M Bujnicki, 2015, RNA.

Ultraviolet Shadowing of RNA Can Cause Significant Chemical Damage in Seconds

Rhiju Das, Wipapat Kladwang, Justine Hum, 2012, Scientific Reports.

Ultraviolet Shadowing of RNA Causes Substantial Non-Poissonian Chemical Damage in Seconds

Rhiju Das, W. Kladwang, J. Hum, 2012, 1202.4794.

A unified mechanism for intron and exon definition and back-splicing

Rhiju Das, Z. Zhou, K. Kappel, 2019, Nature.

Sampling native-like structures of RNA-protein complexes through Rosetta folding and docking

Rhiju Das, Kalli Kappel, Rhiju Das, 2018, bioRxiv.

De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures

M. Rynge, Rhiju Das, W. Kladwang, 2021, Nucleic acids research.

New prediction categories in CASP15

K. Fidelis, J. Moult, Rhiju Das, 2023, Proteins.

The Stanford RNA Mapping Database for sharing and visualizing RNA structure mapping experiments pdf

Julius B. Lucks, Pablo Cordero, Rhiju Das, 2011, ArXiv.

Primerize: automated primer assembly for transcribing non-coding RNA domains

Pablo Cordero, Siqi Tian, Rhiju Das, 2015, Nucleic Acids Res..

Assessment of three-dimensional RNA structure prediction in CASP15

Zhichao Miao, E. Westhof, Rhiju Das, 2023, bioRxiv.

RNA target highlights in CASP15: Evaluation of predicted models by structure providers.

J. Moult, Rhiju Das, J. Wedekind, 2023, Proteins.

Atomic accuracy in predicting and designing noncanonical RNA structure

J. Karanicolas, Rhiju Das, D. Baker, 2010, Nature Methods.

Likelihood-based Fits of Folding Transitions (LiFFT) for Biomolecule Mapping Data

Rhiju Das, Rhiju Das, 2018, bioRxiv.

RNA Structure Refinement using the ERRASER-Phenix pipeline

Rhiju Das, T. Terwilliger, N. Echols, 2013, bioRxiv.

Rosetta in CAPRI rounds 13–19

David Baker, Sarel J Fleishman, Rhiju Das, 2010, Proteins.

RNA Structure Refinement Using the ERRASER-Phenix Pipeline.

Nathaniel Echols, Thomas C Terwilliger, Rhiju Das, 2016, Methods in molecular biology.

Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server.

Rhiju Das, Rhiju Das, J. Yesselman, 2016, Methods in molecular biology.

Chapter 17 RNA Structure Refi nement Using the ERRASER-Phenix Pipeline

Rhiju Das, T. Terwilliger, N. Echols, 2015 .

Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles

Sungroh Yoon, Taehoon Lee, Seungmyung Lee, 2015, Bioinform..

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Brian D. Weitzner, Karen R. Khar, Roland L. Dunbrack, 2020, Nature Methods.

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

Jason W. Labonte, Jeffrey J. Gray, Johanna K. S. Tiemann, 2021, Nature Communications.

Counterion distribution around DNA probed by solution X-ray scattering.

Rhiju Das, I. Millett, S. Doniach, 2003, Physical review letters.

CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps

Rhiju Das, M. Topf, D. Rigden, 2023, bioRxiv.

Prospects for de novo phasing with de novo protein models

Rhiju Das, D. Baker, 2009, Acta crystallographica. Section D, Biological crystallography.

Remeasuring the Double Helix

Rhiju Das, P. Harbury, Rebecca S. Mathew-Fenn, 2008, Science.

Identification and targeting of a pan-genotypic influenza A virus RNA structure that mediates packaging and disease

S. Schaffert, P. Khatri, Rhiju Das, 2021, bioRxiv.

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

Oliver F. Lange, Jeffrey J. Gray, Ian W. Davis, 2011, Methods in enzymology.

Macromolecular modeling with rosetta.

Rhiju Das, D. Baker, 2008, Annual review of biochemistry.

De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes

Rhiju Das, J. Puglisi, G. Skiniotis, 2018, Nature Methods.

Atomic accuracy in predicting and designing non-canonical RNA structure

J. Karanicolas, Rhiju Das, D. Baker, 2010, Nature Methods.

Structure prediction for CASP7 targets using extensive all‐atom refinement with Rosetta@home

Andrew M Wollacott, David E. Kim, Chu Wang, 2007, Proteins.

Understanding the errors of SHAPE-directed RNA structure modeling.

Rhiju Das, W. Kladwang, P. Cordero, 2011, Biochemistry.

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.

Katarzyna J Purzycka, K. Weeks, Zhichao Miao, 2017, RNA.

Assessment of three‐dimensional RNA structure prediction in CASP15

Rhiju Das, D. Rigden, R. Rangan, 2023, Proteins.

Assessment of three-dimensional RNA structure prediction in CASP15

Zhichao Miao, E. Westhof, Rhiju Das, 2023, bioRxiv.

A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA.

Rhiju Das, W. Kladwang, P. Cordero, 2011, RNA.

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

Kyle A. Beauchamp, V. Pande, Rhiju Das, 2012, Journal of chemical theory and computation.

Allosteric mechanism of the V. vulnificus adenine riboswitch resolved by four-dimensional chemical mapping

Rhiju Das, Siqi Tian, W. Kladwang, 2018, eLife.

Ribonanza: deep learning of RNA structure through dual crowdsourcing

Christian A. Choe, John J. Nicol, Rhiju Das, 2024, bioRxiv.

Outcome of a workshop on applications of protein models in biomedical research.

Roland L. Dunbrack, David T. Jones, M. Levitt, 2009, Structure.

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

Magdalena A. Jonikas, R. Altman, D. Herschlag, 2009, RNA.

High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states

Siqi Tian, Rhiju Das, Wipapat Kladwang, 2014, bioRxiv.

Blind tests of RNA–protein binding affinity prediction

D. Herschlag, Rhiju Das, W. Greenleaf, 2019, Proceedings of the National Academy of Sciences.

Computational design of three-dimensional RNA structure and function

Paul D. Carlson, Erik D. Carlson, Alexandra N. Ooms, 2019, Nature Nanotechnology.