Publications by authors named "David A Case"

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Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16.
Rachael C Kretsch, Elisa Posani, Eugene F Baulin, Janusz M Bujnicki, Giovanni Bussi, David A Case

Proteins· November 2025

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Blind prediction of complex water and ion ensembles around RNA in CASP16.
Rachael C Kretsch, Elisa Posani, Eugene F Baulin, Janusz M Bujnicki, Giovanni Bussi, David A Case

bioRxiv· November 2025

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Wavelength dependent photochemistry of an iron dinitrogen hydride complex multiple spectroscopies - competing ejection of axial ligands.
Weibing Dong, Hongxin Wang, Saeed Kamali, David R Tyler, Yisong Guo, David A Case

Chem Sci· August 2025

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Recent Developments in Amber Biomolecular Simulations.
David A Case, David S Cerutti, Vinícius Wilian D Cruzeiro, Thomas A Darden, Robert E Duke

J Chem Inf Model· August 2025

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Validated ligand geometries for macromolecular refinement restraints and molecular mechanics force fields.
Nigel W Moriarty, David A Case, Dorothee Liebschner, Paul D Adams

bioRxiv· August 2025

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Complex water networks visualized by cryogenic electron microscopy of RNA.
Rachael C Kretsch, Shanshan Li, Grigore Pintilie, Michael Z Palo, David A Case

Nature· June 2025

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Selective [9-N] Guanosine for Nuclear Magnetic Resonance Studies of Large Ribonucleic Acids.
Solomon K Attionu, Rita Dill, Michael F Summers, David A Case, Jan Marchant

Chembiochem· June 2025

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The need to implement FAIR principles in biomolecular simulations.
Rommie E Amaro, Johan Åqvist, Ivet Bahar, Federica Battistini, Adam Bellaiche, David A Case

Nat Methods· April 2025

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Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v0.1].
Chapin E Cavender, David A Case, Julian C-H Chen, Lillian T Chong, Daniel A Keedy

ArXiv· March 2025

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Complex Water Networks Visualized through 2.2-2.3 Å Cryogenic Electron Microscopy of RNA.
Rachael C Kretsch, Shanshan Li, Grigore Pintilie, Michael Z Palo, David A Case

bioRxiv· January 2025

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Simulating the Motion Underlying the Mechanism of Thioredoxin Reductase.
Erik R P Zuiderweg, David A Case, Charles H Williams

ACS Omega· July 2024

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Enhanced TROSY Effect in [2- F, 2- C] Adenosine and ATP Analogs Facilitates NMR Spectroscopy of Very Large Biological RNAs in Solution.
Fabian Juen, David Glänzer, Raphael Plangger, Valentina Kugler, Jakob Fleischmann, David A Case

Angew Chem Int Ed Engl· February 2024

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X-ray Crystallography Module in MD Simulation Program Amber 2023. Refining the Models of Protein Crystals.
Oleg Mikhailovskii, Sergei A Izmailov, Yi Xue, David A Case, Nikolai R Skrynnikov

J Chem Inf Model· January 2024

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An RNA excited conformational state at atomic resolution.
Ainan Geng, Laura Ganser, Rohit Roy, Honglue Shi, Supriya Pratihar, David A Case

Nat Commun· December 2023

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AmberTools.
David A Case, Hasan Metin Aktulga, Kellon Belfon, David S Cerutti, G Andrés Cisneros

J Chem Inf Model· October 2023

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MD simulations of macromolecular crystals: Implications for the analysis of Bragg and diffuse scattering.
David A Case

Methods Enzymol· September 2023

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New experimental evidence for pervasive dynamics in proteins.
Erik R P Zuiderweg, David A Case

Protein Sci· May 2023

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Robust total X-ray scattering workflow to study correlated motion of proteins in crystals.
Steve P Meisburger, David A Case, Nozomi Ando

Nat Commun· March 2023

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RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis.
Şölen Ekesan, Erika McCarthy, David A Case, Darrin M York

J Phys Chem B· August 2022

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Molecular dynamics analysis of a flexible loop at the binding interface of the SARS-CoV-2 spike protein receptor-binding domain.
Jonathan K Williams, Baifan Wang, Andrew Sam, Cody L Hoop, David A Case

Proteins· May 2022

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Colicin E1 opens its hinge to plug TolC.
S Jimmy Budiardjo, Jacqueline J Stevens, Anna L Calkins, Ayotunde P Ikujuni, Virangika K Wimalasena, David A Case

Elife· February 2022

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Integral equation models for solvent in macromolecular crystals.
Jonathon G Gray, George M Giambaşu, David A Case, Tyler Luchko

J Chem Phys· January 2022

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Simulations of Kindlin-2 PIP binding domains reveal protonation-dependent membrane binding modes.
Robert D Palmere, David A Case, Andrew J Nieuwkoop

Biophys J· December 2021

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A quantitative model predicts how mA reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions.
Bei Liu, Honglue Shi, Atul Rangadurai, Felix Nussbaumer, Chia-Chieh Chu, David A Case

Nat Commun· August 2021

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Refinement of RNA Structures Using Amber Force Fields.
Jonathon G Gray, David A Case

Crystals (Basel)· July 2021

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