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Author Details

Rhiju Das
Stanford University School of Medicine
2001
148
56
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36227570Auto-DRRAFTER: Automated RNA Modeling Based on Cryo-EM Density.Methods Mol Biol2023
38076883Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses.bioRxiv2023
37994556CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps.Proteins2023
37609268CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps.bioRxiv2023
37876231Assessment of three-dimensional RNA structure prediction in CASP15.Proteins2023
37466021RNA target highlights in CASP15: Evaluation of predicted models by structure providers.Proteins2023
37306011New prediction categories in CASP15.Proteins2023
37162955Assessment of three-dimensional RNA structure prediction in CASP15.bioRxiv2023
36810740Community science designed ribosomes with beneficial phenotypes.Nat Commun2023
36705908RNA 3D Modeling with FARFAR2, Online.Methods Mol Biol2023
35318324Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics.Nat Commun2022
35471911Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular switches.Proc Natl Acad Sci U S A2022
35836020Three-dimensional structure-guided evolution of a ribosome with tethered subunits.Nat Chem Biol2022
35667008Correction to "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design".J Chem Theory Comput2022
36567960Deep learning models for predicting RNA degradation via dual crowdsourcing.Nat Mach Intell2022
36484094Computationally-guided design and selection of high performing ribosomal active site mutants.Nucleic Acids Res2022
36067294Topological crossing in the misfolded <i>Tetrahymena</i> ribozyme resolved by cryo-EM.Proc Natl Acad Sci U S A2022
36192461RNA secondary structure packages evaluated and improved by high-throughput experiments.Nat Methods2022
35982307Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2.Nat Med2022
33963334RNA structure: a renaissance begins?Nat Methods2021
33883742Structure of human telomerase holoenzyme with bound telomeric DNA.Nature2021
33846332Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis.Nat Commun2021
33821271Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics.bioRxiv2021
33821006Functional and structural basis of extreme conservation in vertebrate 5' untranslated regions.Nat Genet2021
33693814De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures.Nucleic Acids Res2021
34492193How to Kinetically Dissect an RNA Machine.Biochemistry2021
34426697Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome.Nat Struct Mol Biol2021
34661102RiboDraw: semiautomated two-dimensional drawing of RNA tertiary structure diagrams.NAR Genom Bioinform2021
34446608Geometric deep learning of RNA structure.Science2021
34591967Correction to 'Theoretical basis for stabilizing messenger RNA through secondary structure design'.Nucleic Acids Res2021
32511306RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses.bioRxiv2020
32743589Cryo-electron Microscopy and Exploratory Antisense Targeting of the 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome.bioRxiv2020
32817241Folding heterogeneity in the essential human telomerase RNA three-way junction.RNA2020
32616928Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures.Nat Methods2020
32217750Transcription polymerase-catalyzed emergence of novel RNA replicons.Science2020
32483333Macromolecular modeling and design in Rosetta: recent methods and frameworks.Nat Methods2020
32371455RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers.RNA2020
30416038Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking.Structure2019
34308269Scientific Discovery Games for Biomedical Research.Annu Rev Biomed Data Sci2019
31640563RNA 3D structure prediction guided by independent folding of homologous sequences.BMC Bioinformatics2019
31796736Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7⿿ÿ resolution.Nat Commun2019
31216023Structure and ligand binding of the glutamine-II riboswitch.Nucleic Acids Res2019
31298841Automated Design of Diverse Stand-Alone Riboswitches.ACS Synth Biol2019
31239056Evaluating riboswitch optimality.Methods Enzymol2019
31239046Using Rosetta for RNA homology modeling.Methods Enzymol2019
31375637Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation.Proc Natl Acad Sci U S A2019
31485080A unified mechanism for intron and exon definition and back-splicing.Nature2019
31427748Computational design of three-dimensional RNA structure and function.Nat Nanotechnol2019
31399592A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites.Nat Commun2019
31247029EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogame.PLoS Comput Biol2019
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Collaborators

David Baker
University of Washington
Co-authored papers 15
Jeffrey J Gray
Johns Hopkins University
Co-authored papers 7
Wah Chiu
Stanford University
Co-authored papers 7
Brian Kuhlman
Co-authored papers 6
Tanja Kortemme
University of California san francisco
Co-authored papers 6
Andriy Kryshtafovych
University of California davis
Co-authored papers 6
William J Greenleaf
Stanford University
Co-authored papers 6
Alain Laederach
University of North Carolina at Chapel Hill
Co-authored papers 6
Grigore Pintilie
Stanford University
Co-authored papers 6
Richard Bonneau
Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation
Co-authored papers 5
Nikolay V Dokholyan
Pennsylvania State University College of Medicine
Co-authored papers 5
Frank DiMaio
University of Washington
Co-authored papers 5
Michael C Jewett
Northwestern University
Co-authored papers 4
Russ B Altman
Stanford University
Co-authored papers 4
Michael S Pacella
Co-authored papers 4
Roland L Dunbrack
Fox Chase Cancer Center
Co-authored papers 4
John Moult
Institute for Bioscience and Biotechnology Research
Co-authored papers 4
Torsten Schwede
University of Basel
Co-authored papers 3
Jens Meiler
Vanderbilt University
Co-authored papers 3
Yi Xiao
Co-authored papers 3
Maya Topf
Leibniz-Institut fur Virologie (LIV)
Co-authored papers 3
Lois Pollack
Cornell University
Co-authored papers 3
Jeliazko R Jeliazkov
Co-authored papers 3
Hahnbeom Park
Co-authored papers 3
Dinshaw J Patel
Memorial Sloan-Kettering Cancer Center
Co-authored papers 3
Michael Brenowitz
Albert Einstein College of Medicine
Co-authored papers 2
Sagar D Khare
The State University of New Jersey
Co-authored papers 2
Oliver F Lange
Center for Integrated Protein Science, Technische Universitat Munchen
Co-authored papers 2
Jacob E Corn
Co-authored papers 2
Krzysztof Fidelis
University of California davis
Co-authored papers 2
Release 1.2