J. Yesselman

发表

Computational design of three-dimensional RNA structure and function

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

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

D. Case, D. Herschlag, H. Al‐Hashimi, 2020, Nature Communications.

Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases.

H. Al‐Hashimi, R. Mehl, S. Scheiner, 2013, Journal of the American Chemical Society.

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

Raghuvir N. Sengupta, D. York, D. Herschlag, 2016, RNA.

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

C. Brooks, R. Trievel, S. Horowitz, 2015, Proteins.

An RNA dynamic ensemble at atomic resolution

D. Case, D. Herschlag, H. Al‐Hashimi, 2020, 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 structure inference through chemical mapping after accidental 1 or intentional mutations 2 3 4

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

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

Charles L. Brooks, Daniel J. Price, Jennifer L. Knight, 2012, J. Comput. Chem..

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

Rhiju Das, J. Yesselman, 2015, bioRxiv.

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

H. Al‐Hashimi, R. Trievel, S. Horowitz, 2011, The Journal of Biological Chemistry.

Computational Design of Asymmetric Three-dimensional RNA Structures and Machines

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

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

E. J. Arthur, Evan J Arthur, C. Brooks, 2011, Proteins.

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

J. Feigon, J. Yesselman, Yaqiang Wang, 2016, Proceedings of the National Academy of Sciences.

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

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

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

Zhipeng Lu, W. A. Velema, J. Yesselman, 2021, Nature Communications.

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

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

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

G. Brewer, A. Tai, Mei-Ling Li, 2021, Science advances.

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

G. Brewer, A. Tai, Mei-Ling Li, 2020, bioRxiv.

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

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

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

Andrew M. Watkins, Wah Chiu, Rhiju Das, 2020, Nature Methods.

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

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

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.

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

Silvi Rouskin, J. Yesselman, Amir Brivanlou, 2022, Nucleic Acids Res..

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

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

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

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

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

Charles L. Brooks, Jennifer L. Knight, Joseph D. Yesselman, 2013, J. Comput. Chem..

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

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

Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server.

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

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

J. Yesselman, C. D. Eichhorn, Momodou B. Camara, 2023, bioRxiv.

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

J. Yesselman, C. D. Eichhorn, Momodou B. Camara, 2023, Nucleic acids research.

Computational design of three-dimensional RNA structure and function

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