David A. Case

The NMR Exchange Format (NEF): Specification and Applications

Eliza Płoskoń, Kumaran Baskaran, Roberto Tejero, Charles D. Schwieters et autres

The NMR Exchange Format (NEF) is a community-driven standard for representing NMR experimental data in a consistent, interoperable, and machine-readable form. Built on the STAR syntax, NEF provides a structured framework for storing and exchanging chemical shifts, peak lists, various types of …

gb, us, es, fr, de, ch, jp, br, ca, be, in, pl (code pays fourni par la source)

FoldaVirus, a knowledge-based icosahedral capsid builder using AlphaFold

Oscar Rojas Labra, David S Montoya-Munoz, Nelly Santoyo-Rivera, Jeffrey G. McDonald et autres

Abstract Coat protein (CP) tertiary structures and their capsid organization of spherical viruses are highly conserved within each virus family. While AlphaFold successfully predicts the tertiary structures of individual CPs, their association to form proper quaternary assemblies cannot be easily accomplished. Here, …

us, mx (code pays fourni par la source)

Replication Package for "Development of an Optimized Parameter Set for Monovalent Ions in the Reference Interaction Site Model of Solvation"

Felipe Silva Carvalho, Alexander McMahon, David A. Case, Tyler Luchko

Research scripts and supporting files for 1D-RISM and 3D-RISM calculations of aqueous monovalent salts, accompanying the paper “Development of an Optimized Parameter Set for Monovalent Ions in the Reference Interaction Site Model of Solvation.” Includes workflow scripts, ion model files, precomputed XVV …

us (code pays fourni par la source)

Replication Package for "Development of an Optimized Parameter Set for Monovalent Ions in the Reference Interaction Site Model of Solvation"

Felipe Silva Carvalho, Alexander McMahon, David A. Case, Tyler Luchko

Research scripts and supporting files for 1D-RISM and 3D-RISM calculations of aqueous monovalent salts, accompanying the paper “Development of an Optimized Parameter Set for Monovalent Ions in the Reference Interaction Site Model of Solvation.” Includes workflow scripts, ion model files, precomputed XVV …

us (code pays fourni par la source)

Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16

Rachael C. Kretsch, Elisa Posani, Eugene F. Baulin, Janusz M. Bujnicki et autres

Biomolecules rely on water and ions for stable folding, but these interactions are often transient, dynamic, or disordered and thus hidden from experiments and evaluation challenges that represent biomolecules as single, ordered structures. Here, we compare blindly predicted ensembles of water and …

us, it, pl, se, in, jp, cn, cl, be (code pays fourni par la source)

Blind prediction of complex water and ion ensembles around RNA in CASP16

Rachael C. Kretsch, Elisa Posani, Eugene F. Baulin, Janusz M. Bujnicki et autres

Abstract Biomolecules rely on water and ions for stable folding, but these interactions are often transient, dynamic, or disordered and thus hidden from experiments and evaluation challenges that represent biomolecules as single, ordered structures. Here, we compare blindly predicted ensembles of water …

us, it, pl, se, in, jp, cn, cl, be, ru (code pays fourni par la source)

Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0]

Chapin E. Cavender, David A. Case, Julian C.‐H. Chen, Lillian T. Chong et autres

This review article provides an overview of structurally oriented experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and room temperature (RT) protein crystallography. We discuss what the observables are, …

us, dk, fi, gb (code pays fourni par la source)

Author response for "Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16 "

Rachael C. Kretsch, Elisa Posani, Eugene F. Baulin, Janusz M. Bujnicki et autres

Complex Water Networks Visualized through Cryogenic Electron Microscopy of RNA

Rachael C. Kretsch, Shanshan Li, Grigore Pintilie, Michael Z. Palo et autres

The stability and function of biomolecules are directly influenced by their myriad interactions with water. Nucleic acids are highly solvated and hence uniquely suited for the investigation of water in near-native conditions using cryogenic electron microscopy (cryo-EM). We determined two cryo-EM maps …

us, cn (code pays fourni par la source)

Validated ligand geometries for macromolecular refinement restraints and molecular mechanics force fields

Nigel W. Moriarty, David A. Case, Dorothée Liebschner, Paul D. Adams

information in the form of restraints. Having accurate geometries of the chemical entities in the sample is paramount for generating accurate chemical restraints and, therefore, accurate macromolecular structures. In particular, it is desirable to have accurate restraints for known and novel ligand …

us (code pays fourni par la source)

Recent Developments in Amber Biomolecular Simulations

David A. Case, David S. Cerutti, Vinícius Wilian D. Cruzeiro, Thomas A. Darden et autres

High Resolution Image Download MS PowerPoint Slide Amber is a molecular dynamics (MD) software package first conceived by Peter Kollman, his lab and collaborators to simulate biomolecular systems. The pmemd module is available as a serial version for central processing units (CPUs), …

us, ca, cn (code pays fourni par la source)

Wavelength dependent photochemistry of an iron dinitrogen hydride complex via multiple spectroscopies - Competing ejection of axial ligands

Weibing Dong, Hongxin Wang, Saeed Kamali, David R. Tyler et autres

Nitrogenase (N2ase) is a critical enzyme which catalyzes the reaction of N2 --> NH3 in nature. Studies on the spectroscopy and photochemistry of trans-[FeII(DMeOPrPE)2(N2)H][BPh4](1) and its isotopomers provide a possible first step to evaluate the geometries and properties of the real N2ase-N2 …

cn, us, jp (code pays fourni par la source)