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

Structure (London), 2019-01, Vol.27 (1), p.140-151.e5

2019

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

Nature methods, 2020-07, Vol.17 (7), p.699

2020

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

Journal of chemical theory and computation, 2017-06, Vol.13 (6), p.3031-3048

2017

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

Nature (London), 2019-09, Vol.573 (7774), p.375-380

2019

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Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor

Quarterly reviews of biophysics, 2015-11, Vol.48 (4), p.479-487

2015

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

Nature communications, 2019-12, Vol.10 (1), p.5511-6, Article 5511

2019

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

Nature communications, 2021-04, Vol.12 (1), p.2165-17, Article 2165

2021

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

BMC bioinformatics, 2019-10, Vol.20 (1), p.512-512, Article 512

2019

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

Molecular cell, 2019-06, Vol.74 (5), p.966-981.e18

2019

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Blind tests of RNA nearest-neighbor energy prediction

Proceedings of the National Academy of Sciences - PNAS, 2016-07, Vol.113 (30), p.8430-8435

2016

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Macromolecular modeling and design in Rosetta: recent methods and frameworks

Nature methods, 2020-07, Vol.17 (7), p.665

2020

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Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution

Nature (London), 2021-08, Vol.596 (7873), p.603-607

2021

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

Proceedings of the National Academy of Sciences - PNAS, 2022-09, Vol.119 (37), p.1-e2209146119

2022

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Auto-DRRAFTER: Automated RNA Modeling Based on Cryo-EM Density

Methods in molecular biology (Clifton, N.J.), 2023, Vol.2568, p.193

2023

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Blind tests of RNA–protein binding affinity prediction

Proceedings of the National Academy of Sciences - PNAS, 2019-04, Vol.116 (17), p.8336-8341

2019

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Architecture of an HIV-1 reverse transcriptase initiation complex

Nature (London), 2018-05, Vol.557 (7706), p.118-122

2018

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

RNA (Cambridge), 2017-02, Vol.23 (2), p.175-188

2017

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

Nature methods, 2018-11, Vol.15 (11), p.947

2018

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Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA

Nature (London), 2022-10, Vol.610 (7932), p.575-581

2022

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DAPTEV: Deep aptamer evolutionary modelling for COVID-19 drug design

PLoS computational biology, 2023-07, Vol.19 (7), p.e1010774-e1010774

2023

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

Nature communications, 2019-12, Vol.10 (1)

2019

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The binding mechanism, multiple binding modes, and allosteric regulation of Staphylococcus aureus Sortase A probed by molecular dynamics simulations

Protein science, 2012-12, Vol.21 (12), p.1858-1871

2012

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Modeling the Structures and Energetics of Rna and Rna-Protein Complexes

Kappel, Kalli

2019

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ProQuest

Distinct Conformational States Underlie Pausing during Initiation of HIV-1 Reverse Transcription

Journal of molecular biology, 2020-07, Vol.432 (16), p.4499-4522

2020

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Blind Predictions of RNA/Protein Relative Binding Affinities

Biophysical journal, 2017-02, Vol.112 (3), p.72a-72a

2017

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

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

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

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

Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor

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

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

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

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

Blind tests of RNA nearest-neighbor energy prediction

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution

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

Auto-DRRAFTER: Automated RNA Modeling Based on Cryo-EM Density

Blind tests of RNA–protein binding affinity prediction

Architecture of an HIV-1 reverse transcriptase initiation complex

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

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

Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA

DAPTEV: Deep aptamer evolutionary modelling for COVID-19 drug design

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

The binding mechanism, multiple binding modes, and allosteric regulation of Staphylococcus aureus Sortase A probed by molecular dynamics simulations

Modeling the Structures and Energetics of Rna and Rna-Protein Complexes

Distinct Conformational States Underlie Pausing during Initiation of HIV-1 Reverse Transcription

Blind Predictions of RNA/Protein Relative Binding Affinities

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