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Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction

Nature communications, 2020-11, Vol.11 (1), p.5531-14, Article 5531

2020

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Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells

Nature communications, 2022-02, Vol.13 (1), p.911-13, Article 911

2022

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Structural conservation in the template/pseudoknot domain of vertebrate telomerase RNA from teleost fish to human

Proceedings of the National Academy of Sciences - PNAS, 2016-08, Vol.113 (35), p.E5125-E5134

2016

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MATCH: An atom-typing toolset for molecular mechanics force fields

Journal of computational chemistry, 2012-01, Vol.33 (2), p.189-202

2012

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

Nature methods, 2020-07, Vol.17 (7), p.699-707

2020

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High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping

Nucleic acids research, 2024-09, Vol.52 (16), p.9953-9965

2024

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Web-based platform for analysis of RNA folding from high throughput chemical probing data

Nucleic acids research, 2022-07, Vol.50 (W1), p.W266-W271

2022

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Automated 3D Design and Evaluation of RNA Nanostructures with RNAMake

Methods in molecular biology (Clifton, N.J.), 2023, Vol.2586, p.251

2023

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An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions

RNA (Cambridge), 2016-01, Vol.22 (1), p.32-48

2016

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Visualizing a two-state conformational ensemble in stem-loop 3 of the transcriptional regulator 7SK RNA

Nucleic acids research, 2024-01, Vol.52 (2), p.940-952

2024

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

Proceedings of the National Academy of Sciences - PNAS, 2019-08, Vol.116 (34), p.16847-16855

2019

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

RNA (Cambridge), 2020-08, Vol.26 (8), p.982-995

2020

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Simulated LC–MS Data Set for Assessing the Metabolomics Data Processing Pipeline Implemented into MVAPACK

Analytical chemistry (Washington), 2024-08, Vol.96 (32), p.12943-12956

2024

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Computational design of three-dimensional RNA structure and function

Nature nanotechnology, 2019-09, Vol.14 (9), p.866-873

2019

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

Nucleic acids research, 2018-01, Vol.46 (D1), p.D375-D379

2018

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

Nucleic acids research, 2015-07, Vol.43 (W1), p.W522-W526

2015

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

Nucleic acids research, 2015-07, Vol.43 (W1), p.W498

2015

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Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server

Methods in molecular biology (Clifton, N.J.), 2016-01, Vol.1490, p.187

2016

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Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures

Proteins, structure, function, and bioinformatics, 2015-03, Vol.83 (3), p.403-410

2015

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Conservation and Functional Importance of Carbon–Oxygen Hydrogen Bonding in AdoMet-Dependent Methyltransferases

Journal of the American Chemical Society, 2013-10, Vol.135 (41), p.15536-15548

2013

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Direct Evidence for Methyl Group Coordination by Carbon-Oxygen Hydrogen Bonds in the Lysine Methyltransferase SET7/9

The Journal of biological chemistry, 2011-05, Vol.286 (21), p.18658-18663

2011

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Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes

Journal of computational chemistry, 2013-04, Vol.34 (11), p.893-903

2013

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Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures

Science advances, 2021-11, Vol.7 (48), p.eabl6096-eabl6096

2021

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High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping

Biophysical journal, 2024-02, Vol.123 (3), p.365a-365a

2024

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Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics

Proteins, structure, function, and bioinformatics, 2011-12, Vol.79 (12), p.3276-3286

2011

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Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction

Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells

Structural conservation in the template/pseudoknot domain of vertebrate telomerase RNA from teleost fish to human

MATCH: An atom-typing toolset for molecular mechanics force fields

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

High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping

Web-based platform for analysis of RNA folding from high throughput chemical probing data

Automated 3D Design and Evaluation of RNA Nanostructures with RNAMake

An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions

Visualizing a two-state conformational ensemble in stem-loop 3 of the transcriptional regulator 7SK RNA

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

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

Simulated LC–MS Data Set for Assessing the Metabolomics Data Processing Pipeline Implemented into MVAPACK

Computational design of three-dimensional RNA structure and function

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

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

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

Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server

Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures

Conservation and Functional Importance of Carbon–Oxygen Hydrogen Bonding in AdoMet-Dependent Methyltransferases

Direct Evidence for Methyl Group Coordination by Carbon-Oxygen Hydrogen Bonds in the Lysine Methyltransferase SET7/9

Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes

Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures

High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping

Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics

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