List of works - Rhiju Das

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

scientific article published on 08 May 2019

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

scientific article published on 09 August 2019

A maximum-likelihood approach to removing radio sources from observations of the Sunyaev--Zel'dovich effect, with application to Abell 611

scholarly article

A measurement of H0 from Ryle Telescope, ASCA and ROSAT observations of Abell 773

scientific article

A molecular ruler for measuring quantitative distance distributions

scientific article

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

scientific article

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

scientific article published in September 2010

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

scientific article

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

scientific article

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

scientific article published on 04 September 2019

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

scientific article published on 02 July 2020

Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design

scientific article (publication date: 2013)

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

scientific article published on 28 February 2013

Allosteric Mechanism of theV. vulnificusAdenine Riboswitch Resolved by Four-dimensional Chemical Mapping

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

scientific article published on 15 February 2018

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

scientific article published on 24 May 2018

An RNA Mapping DataBase for curating RNA structure mapping experiments

scientific article

An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling

scientific article published on 5 December 2011

Anomalous reverse transcription through chemical modifications in polyadenosine stretches

scientific article published on 14 May 2020

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

scientific article

Atomic accuracy in predicting and designing noncanonical RNA structure

scientific article

Atomic-accuracy prediction of protein loop structures through an RNA-inspired Ansatz.

scientific article

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

scientific article published on 01 October 2018

Automated Design of Diverse Stand-Alone Riboswitches

scientific article published on 29 July 2019

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

scientific article

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

scientific article

Automated de novo prediction of native-like RNA tertiary structures

scientific article

Bayesian energy landscape tilting: towards concordant models of molecular ensembles

scientific article published on March 2014

Blind prediction of noncanonical RNA structure at atomic accuracy

Blind prediction of noncanonical RNA structure at atomic accuracy.

scientific article published on 25 May 2018

Blind predictions of DNA and RNA tweezers experiments with force and torque

scientific article

Blind tests of RNA nearest-neighbor energy prediction

scientific article

Blind tests of RNA-protein binding affinity prediction

scientific article published on 08 April 2019

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

scientific article

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

scientific article

Compact RNA sensors for increasingly complex functions of multiple inputs

scientific article published on 16 January 2024

Computational design of three-dimensional RNA structure and function

scientific article published on 19 August 2019

Consistent global structures of complex RNA states through multidimensional chemical mapping

scientific article

Controllable molecular motors engineered from myosin and RNA.

scientific article published on 6 November 2017

Correcting pervasive errors in RNA crystallography through enumerative structure prediction

scientific article

Correction: Consistent global structures of complex RNA states through multidimensional chemical mapping

scientific article published on 21 July 2015

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

scientific article published on 16 December 2019

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

scientific article

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

scientific article published on 03 December 2019

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

scientific article published on 20 July 2020

De novo 3D models of SARS-CoV-2 RNA elements and small-molecule-binding RNAs to guide drug discovery

scientific article published on 16 April 2020

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

scholarly article by Kalli Kappel published in October 2018

De novo3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures

scientific article

Detection of a cosmic microwave background decrement towards a cluster of mJy radio sources

scholarly article

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

scientific article published on June 2005

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

scientific article

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

scientific article published on 29 November 2021

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

scientific article published on 27 June 2019

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

Evaluating riboswitch optimality

scientific article published on 18 June 2019

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

scientific article published in May 2003

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

scientific article published on 11 June 2020

Feature Selection Methods for Improving Protein Structure Prediction with Rosetta ⬇️

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

scientific article published on 19 August 2020

Four small puzzles that Rosetta doesn't solve

scientific article published on 20 May 2011

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

scientific article published on 22 November 2017

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

scientific article published on 05 April 2021

HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis

scientific article (publication date: July 2013)

HiTRACE: high-throughput robust analysis for capillary electrophoresis

scientific article published on 10 May 2011

Hidden Structural Modules in a Cooperative RNA Folding Transition.

scientific article published in March 2018

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

scientific article published on 28 June 2018

High-resolution structure prediction and the crystallographic phase problem

scientific article

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

scientific article

LIkelihood-based Fits of Folding Transitions (LIFFT) for Biomolecule Mapping Data

scholarly article published 3 April 2018

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

scientific article published on 12 April 2021

Macromolecular modeling and design in Rosetta: recent methods and frameworks

scientific article published on 01 June 2020

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

scientific article

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

scientific article

Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server

scientific article published on January 2016

Modeling complex RNA tertiary folds with Rosetta

scientific article

Observations of the Sunyaev-Zel'dovich effect in the z=0.78 cluster MS 1137.5+6625

scholarly article

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

scientific article (publication date: 13 February 2009)

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

scientific article

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

scientific article published on 20 May 2015

Principles for Predicting RNA Secondary Structure Design Difficulty

scientific article

Principles of RNA Compaction: Insights from the Equilibrium Folding Pathway of the P4-P6 RNA Domain in Monovalent Cations

scholarly article by Keiji Takamoto published in November 2004

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

scientific article

Prospects for de novo phasing with de novo protein models

scientific article published on 20 January 2009

Publisher Correction: Controllable molecular motors engineered from myosin and RNA.

scientific article published on 2 March 2018

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

scientific article

Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference

scientific article

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

scientific article published on 22 October 2019

RNA Structure Refinement Using the ERRASER-Phenix Pipeline

scientific article published on January 2016

RNA design rules from a massive open laboratory

scientific article

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

scientific article (preprint)

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

scientific article published on 12 May 2020

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

scientific article

RNA structure inference through chemical mapping after accidental or intentional mutations

scientific article

RNA structure inference through chemical mapping after accidental or intentional mutations

RNA structure through multidimensional chemical mapping

scientific article published on January 2016

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

scientific article published on 16 April 2015

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

scientific article

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

scientific article published on 05 May 2020

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

scientific article published on 23 February 2012

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

scientific article published on 11 May 2015

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

scientific article (publication date: 2011)

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

scientific article published on 07 June 2018

Remeasuring the double helix

scientific article published on October 2008

Remodeling a β-peptide bundle

article

Response to Comment on "Remeasuring the Double Helix"

scientific article published in Science

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

scientific article published in Nature Communications

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

scientific article

Rosetta in CAPRI rounds 13-19. ⬇️

scientific article published on November 2010

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

scientific article

Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking

scientific article published on 08 November 2018

Scientific rigor through videogames.

scientific article published on 6 October 2014

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

scientific article published on January 2008

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

scientific article published on 02 August 2019

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

scientific article (publication date: 2013)

Sharing and archiving nucleic acid structure mapping data

scientific article (publication date: July 2011)

Simultaneous prediction of protein folding and docking at high resolution

scientific article published on 28 October 2009

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

scientific article published on 15 November 2016

Spatial distribution of competing ions around DNA in solution.

scientific article published on 7 December 2004

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

scientific article published on 29 March 2019

Standardization of RNA chemical mapping experiments

scientific article (publication date: 20 May 2014)

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

scholarly article

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

scientific article published on 13 October 2006

Structure and ligand binding of the glutamine-II riboswitch

scientific article published on 01 August 2019

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

scientific article published on 02 March 2014

Structure of human telomerase holoenzyme with bound telomeric DNA

scientific article published on 21 April 2021

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

scientific article

Structure prediction for CASP8 with all-atom refinement using Rosetta.

scientific article

The Fastest Global Events in RNA Folding: Electrostatic Relaxation and Tertiary Collapse of the Tetrahymena Ribozyme

scientific article published on 01 September 2003

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

scientific article published on 21 April 2017

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

scientific article

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

scientific article published on 15 August 2006

Theoretical basis for stabilizing messenger RNA through secondary structure design

scientific article published on 24 August 2020

Transcription polymerase-catalyzed emergence of novel RNA replicons

scientific article

Ultraviolet shadowing of RNA can cause significant chemical damage in seconds

scientific article published on 18 July 2012

Understanding nucleic acid-ion interactions

scientific article

Understanding the errors of SHAPE-directed RNA structure modeling

scientific article

Updates to the RNA mapping database (RMDB), version 2.

scientific article published on 9 October 2017

Using Rosetta for RNA homology modeling

scientific article published on 11 June 2019

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

scientific article

List of works by Rhiju Das

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

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

A maximum-likelihood approach to removing radio sources from observations of the Sunyaev--Zel'dovich effect, with application to Abell 611

A measurement of H0 from Ryle Telescope, ASCA and ROSAT observations of Abell 773

A molecular ruler for measuring quantitative distance distributions

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

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

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

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

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

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

Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design

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

Allosteric Mechanism of theV. vulnificusAdenine Riboswitch Resolved by Four-dimensional Chemical Mapping

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

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

An RNA Mapping DataBase for curating RNA structure mapping experiments

An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling

Anomalous reverse transcription through chemical modifications in polyadenosine stretches

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

Atomic accuracy in predicting and designing noncanonical RNA structure

Atomic-accuracy prediction of protein loop structures through an RNA-inspired Ansatz.

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

Automated Design of Diverse Stand-Alone Riboswitches

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

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

Automated de novo prediction of native-like RNA tertiary structures

Bayesian energy landscape tilting: towards concordant models of molecular ensembles

Blind prediction of noncanonical RNA structure at atomic accuracy

Blind prediction of noncanonical RNA structure at atomic accuracy.

Blind predictions of DNA and RNA tweezers experiments with force and torque

Blind tests of RNA nearest-neighbor energy prediction

Blind tests of RNA-protein binding affinity prediction

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

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

Compact RNA sensors for increasingly complex functions of multiple inputs

Computational design of three-dimensional RNA structure and function

Consistent global structures of complex RNA states through multidimensional chemical mapping

Controllable molecular motors engineered from myosin and RNA.

Correcting pervasive errors in RNA crystallography through enumerative structure prediction

Correction: Consistent global structures of complex RNA states through multidimensional chemical mapping

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

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

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

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

De novo 3D models of SARS-CoV-2 RNA elements and small-molecule-binding RNAs to guide drug discovery

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

De novo3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures

Detection of a cosmic microwave background decrement towards a cluster of mJy radio sources

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

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

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

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

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

Evaluating riboswitch optimality

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

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

Feature Selection Methods for Improving Protein Structure Prediction with Rosetta ⬇️

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

Four small puzzles that Rosetta doesn't solve

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

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

HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis

HiTRACE: high-throughput robust analysis for capillary electrophoresis

Hidden Structural Modules in a Cooperative RNA Folding Transition.

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

High-resolution structure prediction and the crystallographic phase problem

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

LIkelihood-based Fits of Folding Transitions (LIFFT) for Biomolecule Mapping Data

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

Macromolecular modeling and design in Rosetta: recent methods and frameworks

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

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

Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server

Modeling complex RNA tertiary folds with Rosetta

Observations of the Sunyaev-Zel'dovich effect in the z=0.78 cluster MS 1137.5+6625

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

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

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