Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide. - Winkler, Lauren; Cheatham, Thomas E. (J. Chem. Inf. Model., 2023)

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; et al. (J. Chem. Inf. Model., 2023)

Professionalization of Research Computing and Data: An Expanded Agenda. - Cutcher-Gershenfeld, Joel; Battelle, Torey; Brunson, Dana; Cheatham, Thomas E.; Fosso-Tande, Jacob; Jennewein, Douglas M.; Ma, Julie; Michael, Lauren A.; Middelkoop, Timothy; Neeman, Henry; Schmitz, Patrick (2023)

Building the Research Innovation Workforce: Challenges and Recommendations from a Virtual Workshop to Advance the Research Computing Community✱. - Hacker, Thomas J.; Smith, Preston M.; Brunson, Dana; Arafune, Lisa; Cheatham, Thomas E.; Deelman, Ewa (2022)

Advancing the Workforce That Supports Computationally and Data Intensive Research. - Schmitz, Patrick; Yockel, Scott; Mizumoto, Claire; Cheatham, Thomas E.; Brunson, Dana (Comput. Sci. Eng., 2021)

The Connect.Cyberinfrastructure Portal. - Ma, Julie; Akbar, Sarah; Battelle, Torey; Brandt, Kevin L.; Brown, Eric; Brunson, Dana; Chakravorty, Dhruva; Cheatham, Thomas E.; Chitre, Bhushan; Maestro, Adrian Del; Elledge, Andrea; Gazula, Vikram; et al. (2021)

Leveraging a research computing and data capabilities model for strategic decision-making. - Schmitz, Patrick; Brunson, Dana; Krovitz, Gail; Cheatham, Thomas E.; Mizumoto, Claire (2020)

A Research Computing and Data Capabilities Model for Strategic Decision-Making. - Schmitz, Patrick; Mizumoto, Claire; Hicks, John; Brunson, Dana; Krovitz, Gail; Bottum, James B.; Cutcher-Gershenfeld, Joel; Wetzel, Karen; Cheatham, Thomas E. (2020)

Fostering Collaboration Among Organizations in the Research Computing and Data Ecosystem. - Geva, Sharon Broude; Brunson, Dana; Cheatham, Thomas E., III; Deaton, James; Griffioen, James; Hillegas, Curtis W.; Jennewein, Douglas M.; Krovitz, Gail; Magle, Tobin; Schmitz, Patrick; Tomko, Karen; Wilgenbusch, James C. (2020)

Assessment of financial returns on investments in cyberinfrastructure facilities: A survey of current methods. - Stewart, Craig A.; Hancock, David Y.; Wernert, Julie; Furlani, Thomas R.; Lifka, David; Sill, Alan; Berente, Nicholas; McMullen, Donald F.; Cheatham, Thomas E.; Apon, Amy W.; Payne, Ron; Slavin, Shawn D. (2019)

Improving regional cyberinfrastructure services through collaboration: Cyberteam for the Rocky Mountain Advanced Computing Consortium. - Monaghan, Andrew J.; Milash, Brett; Magle, Tobin; Hauser, Thomas; Cheatham, Thomas E.; Burns, Patrick J.; Knuth, Shelley; Orendt, Anita M.; White, Suzi; Paschal, Dawn; Siegel, Howard Jay; Kaiser, Timothy; et al. (2019)

Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data. - Roe, Daniel R.; Cheatham, Thomas E., III (J. Comput. Chem., 2018)

Task-parallel Analysis of Molecular Dynamics Trajectories. - Paraskevakos, Ioannis; Luckow, André; Khoshlessan, Mahzad; Chantzialexiou, George; Cheatham, Thomas E.; Beckstein, Oliver; Fox, Geoffrey C.; Jha, Shantenu (2018)

Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences. - Zgarbová, Marie; Jurecka, Petr; Lankas, Filip; Cheatham, Thomas E., III; Sponer, Jirí; Otyepka, Michal (J. Chem. Inf. Model., 2017)

Polyhedral Compilation Support for C++ Features: A Case Study with CPPTRAJ. - Roy, Amit; Roe, Daniel R.; Hall, Mary W.; Cheatham, Thomas E. (2017)

Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations. - Heidari, Zahra; Roe, Daniel R.; Galindo-Murillo, Rodrigo; Ghasemi, Jahan B.; Cheatham, Thomas E., III (J. Chem. Inf. Model., 2016)

The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis. - Cheatham, Thomas E., III; Roe, Daniel R. (Comput. Sci. Eng., 2015)

Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing. - Thibault, Julien C.; Roe, Daniel R.; Facelli, Julio C.; Cheatham, Thomas E., III (J. Cheminformatics, 2014)

Structural and Energetic Analysis of 2-Aminobenzimidazole Inhibitors in Complex with the Hepatitis C Virus IRES RNA Using Molecular Dynamics Simulations. - Henriksen, Niel M.; Hayatshahi, Hamed S.; Davis, Darrell R.; Cheatham, Thomas E., III (J. Chem. Inf. Model., 2014)

iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings. - Thibault, Julien C.; Cheatham, Thomas E., III; Facelli, Julio C. (J. Chem. Inf. Model., 2014)

iBIOMES: Managing and Sharing Biomolecular Simulation Data in a Distributed Environment. - Thibault, Julien C.; Facelli, Julio C.; Cheatham, Thomas E., III (J. Chem. Inf. Model., 2013)

Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle. - Shahrokh, Kiumars; Orendt, Anita M.; Yost, Garold S.; Cheatham, Thomas E., III (J. Comput. Chem., 2012)

RNA structure refinement and force field evaluation using molecular dynamics simulations. - Henriksen, Niel M.; Cheatham, Thomas E., III (2011)

Computational Science and Engineering Online (CSE-Online): A Cyber-Infrastructure for Scientific Computing. - Truong, Thanh N.; Nayak, Manohar; Huynh, Hung H.; Cook, Tom; Mahajan, Priya; Tran, Le-Thuy T.; Bharath, Jannu; Jain, Shrish; Pham, Ha B.; Boonyasiriwat, Chaiwoot; Nguyen, Nhat; Andersen, Evan; et al. (J. Chem. Inf. Model., 2006)

The Amber biomolecular simulation programs. - Case, David A.; Cheatham, Thomas E., III; Darden, Tom; Gohlke, Holger; Luo, Ray; Merz, Kenneth M., Jr.; Onufriev, Alexey; Simmerling, Carlos; Wang, Bing; Woods, Robert J. (J. Comput. Chem., 2005)

The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition. - Harvey, Stephen C.; Tan, Robert K.-Z.; Cheatham, Thomas E., III (J. Comput. Chem., 1998)

Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program. - Crowley, Michael F.; Darden, Thomas A.; Cheatham, Thomas E., III; Deerfield, David W., II (J. Supercomput., 1997)

Particle-Mesh Based Methods for Fast Ewald Summation in Molecular Dynamics Simulations. - Darden, Thomas A.; Pedersen, Lee G.; Toukmaji, Abdulnour Y.; Crowley, Michael F.; Cheatham, Thomas E. (1997)

Bulk synchronous parallel computing-a paradigm for transportable software. - Cheatham, Thomas E.; Fahmy, Amr F.; Stefanescu, Dan C.; Valiant, Leslie G. (1995)

General Purpose Optimization Technology. - Cheatham, Thomas E.; Fahmy, Amr F.; Stefanescu, Dan C. (1995)

A Suite of Analysis Tools Based on a General Purpose Abstract Interpreter. - Cheatham, Thomas E.; Gao, Haiming; Stefanescu, Dan C. (1994)

H-BSP - A General Purpose Parallel Computing Environment. - Cheatham, Thomas E.; Fahmy, Amr F.; Stefanescu, Dan C. (1994)

Supporting multiple evolving compilers. - Cheatham, Thomas E.; Fahmy, Amr F.; Stefanescu, Dan C. (1994)

Common runtime support for high-performance parallel languages. - Fox, Geoffrey C.; Ranka, Sanjay; Scott, Michael L.; Malony, Allen D.; Browne, James C.; Chen, Marina C.; Choudhary, Alok N.; Cheatham, Thomas E.; Cuny, Janice E.; Eigenmann, Rudolf; Fahmy, Amr F.; Foster, Ian T.; et al. (1993)

A Suite of Optimizers Based on Abstract Interpretation. - Cheatham, Thomas E.; Stefanescu, Dan C. (1992)

Efficient Execution of Homogeneous Tasks with Unequal Run Times on the Connection Machine. - Bestavros, Azer; Cheatham, Thomas E. (1991)

Parallel bin packing using first fit and k-delayed best-fit heuristics. - Bestavros, Azer; Cheatham, Thomas E.; Stefanescu, Dan C. (1990)

Compiling techniques. - Cheatham, Thomas E. (Commun. ACM, 1966)