PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Roe, Daniel R, Cheatham, Thomas E
Published in Journal of chemical theory and computation (09.07.2013)
Published in Journal of chemical theory and computation (09.07.2013)
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Journal Article
Assessing the Current State of Amber Force Field Modifications for DNA
Galindo-Murillo, Rodrigo, Robertson, James C, Zgarbová, Marie, Šponer, Jiří, Otyepka, Michal, Jurečka, Petr, Cheatham, Thomas E
Published in Journal of chemical theory and computation (09.08.2016)
Published in Journal of chemical theory and computation (09.08.2016)
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Journal Article
Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B‑DNA
Zgarbová, Marie, Šponer, Jiří, Otyepka, Michal, Cheatham, Thomas E., Galindo-Murillo, Rodrigo, Jurečka, Petr
Published in Journal of chemical theory and computation (08.12.2015)
Published in Journal of chemical theory and computation (08.12.2015)
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Journal Article
Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide
Winkler, Lauren, Cheatham, Thomas E.
Published in Journal of chemical information and modeling (24.04.2023)
Published in Journal of chemical information and modeling (24.04.2023)
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Journal Article
Structures and Dynamics of DNA Mini-Dumbbells Are Force Field Dependent
Winkler, Lauren, Galindo-Murillo, Rodrigo, Cheatham, Thomas E.
Published in Journal of chemical theory and computation (25.04.2023)
Published in Journal of chemical theory and computation (25.04.2023)
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Journal Article
AmberTools
Case, David A., Aktulga, Hasan Metin, Belfon, Kellon, Cerutti, David S., Cisneros, G. Andrés, Cruzeiro, Vinícius Wilian D., Forouzesh, Negin, Giese, Timothy J., Götz, Andreas W., Gohlke, Holger, Izadi, Saeed, Kasavajhala, Koushik, Kaymak, Mehmet C., King, Edward, Kurtzman, Tom, Lee, Tai-Sung, Li, Pengfei, Liu, Jian, Luchko, Tyler, Luo, Ray, Manathunga, Madushanka, Machado, Matias R., Nguyen, Hai Minh, O’Hearn, Kurt A., Onufriev, Alexey V., Pan, Feng, Pantano, Sergio, Qi, Ruxi, Rahnamoun, Ali, Risheh, Ali, Schott-Verdugo, Stephan, Shajan, Akhil, Swails, Jason, Wang, Junmei, Wei, Haixin, Wu, Xiongwu, Wu, Yongxian, Zhang, Shi, Zhao, Shiji, Zhu, Qiang, Cheatham, Thomas E., Roe, Daniel R., Roitberg, Adrian, Simmerling, Carlos, York, Darrin M., Nagan, Maria C., Merz, Kenneth M.
Published in Journal of chemical information and modeling (23.10.2023)
Published in Journal of chemical information and modeling (23.10.2023)
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Journal Article
Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields
Bergonzo, Christina, Henriksen, Niel M, Roe, Daniel R, Cheatham, 3rd, Thomas E
Published in RNA (Cambridge) (01.09.2015)
Published in RNA (Cambridge) (01.09.2015)
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Journal Article
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
Zgarbová, Marie, Otyepka, Michal, Šponer, Jiří, Mládek, Arnošt, Banáš, Pavel, Cheatham, Thomas E, Jurečka, Petr
Published in Journal of chemical theory and computation (13.09.2011)
Published in Journal of chemical theory and computation (13.09.2011)
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Journal Article
Improved Force Field Parameters Lead to a Better Description of RNA Structure
Bergonzo, Christina, Cheatham, Thomas E
Published in Journal of chemical theory and computation (08.09.2015)
Published in Journal of chemical theory and computation (08.09.2015)
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Journal Article
Molecular Modeling of Single- and Double-Hydrocarbon-Stapled Coiled-Coil Inhibitors against Bcr-Abl: Toward a Treatment Strategy for CML
Lima, Maria Carolina P., Hornsby, Braxten D., Lim, Carol S., Cheatham, Thomas E.
Published in The journal of physical chemistry. B (11.07.2024)
Published in The journal of physical chemistry. B (11.07.2024)
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Journal Article
Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters
Zgarbová, Marie, Luque, F. Javier, Šponer, Jiří, Cheatham, Thomas E, Otyepka, Michal, Jurečka, Petr
Published in Journal of chemical theory and computation (14.05.2013)
Published in Journal of chemical theory and computation (14.05.2013)
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Journal Article