Thomas E. Cheatham

Parameterizing modified nucleic acids for molecular simulations in the AMBER MD software environment [Article v1.0]

Rodrigo Galindo‐Murillo, Akanksha Manghrani, Daniel R. Roe, Olivia Love et autres

Parameterizing modified nucleic acids is a difficult but necessary task for expanding the simulated space of oligonucleotides, including both naturally occurring structures and those with pharmaceutical relevance. In lieu of expensive and difficult chemical synthesis in the laboratory, computer simulations are often …

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

Rachael C. Kretsch, Elisa Posani, Eugene F. Baulin, Janusz Marek 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 …

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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 Marek 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 …

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

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

Application of Computed FTIR Spectra of Nucleotide Monophosphates to RNA Force Field Refinement

Nathan D. Levinzon, Thomas E. Cheatham

We use the Hessian Matrix reconstruction (HMR) method to compute Fourier transform infrared (FTIR) spectra in the amide I region of nucleotide monophosphates solvated in TIP3P water and in OPC water from molecular dynamics simulations with the Amber OL3/OL15 force fields, and …

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Recent Developments in Amber Biomolecular Simulations

David Andrew 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), …

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Correction to “Molecular Modeling of Single- and Double-Hydrocarbon-Stapled Coiled-Coil Inhibitors against Bcr-Abl: Toward a Treatment Strategy for CML”

Maria Carolina P. Lima, Braxten D. Hornsby, Carol Sunghye Lim, Thomas E. Cheatham

The need to implement FAIR principles in biomolecular simulations

Rommie Elizabeth Amaro, Johan Åqvist, İvet Bahar, Federica Battistini et autres

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modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields

Olivia Love, Rodrigo Galindo‐Murillo, Daniel R. Roe, Pablo Daniel Dans et autres

Modified nucleic acids have surged as a popular therapeutic route, emphasizing the importance of nucleic acid research in drug discovery and development. Beyond well-known RNA vaccines, antisense oligonucleotides and aptamers can incorporate various modified nucleic acids to target specific biomolecules for various …

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The need to implement FAIR principles in biomolecular simulations

Rommie Elizabeth Amaro, Johan Åqvist, İvet Bahar, Federica Battistini et autres

This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necessity of a collaborative effort to create, establish, and sustain a database that …

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Molecular Modeling of Single- and Double-Hydrocarbon-Stapled Coiled-Coil Inhibitors against Bcr-Abl: Toward a Treatment Strategy for CML

Maria Carolina P. Lima, Braxten D. Hornsby, Carol Sunghye Lim, Thomas E. Cheatham

High Resolution Image Download MS PowerPoint Slide The chimeric oncoprotein Bcr-Abl is the causative agent of virtually all chronic myeloid leukemias and a subset of acute lymphoblastic leukemias. As a result of the so-called Philadelphia chromosome translocation t(9;22), Bcr-Abl manifests as a …

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The mechanism of covalent inhibition of LAR phosphatase by illudalic acid

Daniel T. Hansen, Nicole J. Rueb, Nathan D. Levinzon, Thomas E. Cheatham et autres

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