Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins von Cheatham, T. E. III, Miller, J. L, Fox, T, Darden, T. A, Kollman, P. A

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Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles von Zgarbová, Marie, Otyepka, Michal, Šponer, Jiří, Mládek, Arnošt, Banáš, Pavel, Cheatham, Thomas E, Jurečka, Petr

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Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields von Fadrná, Eva, Špačková, Nad’a, Sarzyñska, Joanna, Koča, Jaroslav, Orozco, Modesto, Cheatham, Thomas E, Kulinski, Tadeusz, Šponer, Jiří

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Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices von Srinivasan, Jayashree, Cheatham, Thomas E, Cieplak, Piotr, Kollman, Peter A, Case, David A

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Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise von Cheatham III, Thomas E., Young, Matthew A.

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Molecular Dynamics Simulations and Thermodynamics Analysis of DNA−Drug Complexes. Minor Groove Binding between 4‘,6-Diamidino-2-phenylindole and DNA Duplexes in Solution von Špačková, Nad'a, Cheatham, Thomas E, Ryjáček, Filip, Lankaš, Filip, van Meervelt, Luc, Hobza, Pavel, Šponer, Jiří

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DNA Deformability at the Base Pair Level von Lankaš, Filip, Šponer, Jiří, Langowski, Jörg, Cheatham, Thomas E

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A Molecular Level Picture of the Stabilization of A-DNA in Mixed Ethanol--Water Solutions von Cheatham, Thomas E., Crowley, Michael F., Fox, Thomas, Kollman, Peter A.

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Reference Simulations of Noncanonical Nucleic Acids with Different x Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA von Krepl, M, Zgarbova, M, Stadlbauer, P, Otyepka, M, Banas, P, Koca, J, Cheatham, TE III, Jurecka, P, Sponer, J

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Assessing the Current State of Amber Force Field Modifications for DNA von Galindo-Murillo, Rodrigo, Robertson, James C, Zgarbová, Marie, Šponer, Jiří, Otyepka, Michal, Jurečka, Petr, Cheatham, Thomas E

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Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle von Shahrokh, Kiumars, Orendt, Anita, Yost, Garold S., Cheatham III, Thomas E.

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Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide von Winkler, Lauren, Cheatham, Thomas E.

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Twenty-five years of nucleic acid simulations von Cheatham III, Thomas E., Case, David A.

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The Amber biomolecular simulation programs von Case, David A., Cheatham III, Thomas E., Darden, Tom, Gohlke, Holger, Luo, Ray, Merz Jr, Kenneth M., Onufriev, Alexey, Simmerling, Carlos, Wang, Bing, Woods, Robert J.

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van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD von Love, Olivia, Winkler, Lauren, Cheatham, Thomas E.

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Structures and Dynamics of DNA Mini-Dumbbells Are Force Field Dependent von Winkler, Lauren, Galindo-Murillo, Rodrigo, Cheatham, Thomas E.

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Assessment of A- to B- DNA Transitions Utilizing the Drude Polarizable Force Field von Winkler, Lauren, Galindo-Murillo, Rodrigo, Cheatham, Thomas E.

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Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide von Bergonzo, Christina, Henriksen, Niel M, Roe, Daniel R, Swails, Jason M, Roitberg, Adrian E, Cheatham, Thomas E

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Molecular Modeling of Single- and Double-Hydrocarbon-Stapled Coiled-Coil Inhibitors against Bcr-Abl: Toward a Treatment Strategy for CML von Lima, Maria Carolina P., Hornsby, Braxten D., Lim, Carol S., Cheatham, Thomas E.

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Insight into G-DNA Structural Polymorphism and Folding from Sequence and Loop Connectivity through Free Energy Analysis von Cang, Xiaohui, Šponer, Jiří, Cheatham, III, Thomas E

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