David A. Case - researchr alias

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Viewing Publication 1 - 25 from 25

2024

X-ray Crystallography Module in MD Simulation Program Amber 2023. Refining the Models of Protein CrystalsOleg Mikhailovskii, Sergei A. Izmailov, Yi Xue, David A. Case, Nikolai R. Skrynnikov. jcisd, 64(1):18-25, January 2024. [doi]

2023

2018

GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New FeaturesTai-Sung Lee, David S. Cerutti, Dan Mermelstein, Charles Lin, Scott Legrand, Timothy J. Giese, Adrian E. Roitberg, David A. Case, Ross C. Walker, Darrin M. York. jcisd, 58(10):2043-2050, 2018. [doi]

NGLview-interactive molecular graphics for Jupyter notebooksHai Nguyen, David A. Case, Alexander S. Rose. bioinformatics, 34(7):1241-1242, 2018. [doi]

2017

2016

The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEPYuan Hu, Brad Sherborne, Tai-Sung Lee, David A. Case, Darrin M. York, Zhuyan Guo. jcamd, 30(7):533-539, 2016. [doi]

2015

DOCK 6: Impact of new features and current docking performanceWilliam J. Allen, Trent E. Balius, Sudipto Mukherjee, Scott R. Brozell, Demetri Moustakas, P. Therese Lang, David A. Case, Irwin D. Kuntz, Robert C. Rizzo. jcc, 36(15):1132-1156, 2015. [doi]

2012

Evaluation of DOCK 6 as a pose generation and database enrichment toolScott R. Brozell, Sudipto Mukherjee, Trent E. Balius, Daniel R. Roe, David A. Case, Robert C. Rizzo. jcamd, 26(6):749-773, 2012. [doi]

Energetic Selection of Topology in FerredoxinsJ. Dongun Kim, Agustina Rodriguez-Granillo, David A. Case, Vikas Nanda, Paul G. Falkowski. ploscb, 8(4), 2012. [doi]

2011

A Grid-enabled web portal for NMR structure refinement with AMBERIvano Bertini, David A. Case, Lucio Ferella, Andrea Giachetti, Antonio Rosato. bioinformatics, 27(17):2384-2390, 2011. [doi]

Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformationsThomas Steinbrecher, InSuk Joung, David A. Case. jcc, 32(15):3253-3263, 2011. [doi]

2008

The implementation of a fast and accurate QM/MM potential method in AmberRoss C. Walker, Michael F. Crowley, David A. Case. jcc, 29(7):1019-1031, 2008. [doi]

2006

Second derivatives in generalized Born theoryRussell A. Brown, David A. Case. jcc, 27(14):1662-1675, 2006. [doi]

Low-Resolution Molecular Dynamics Simulations of the 30S Ribosomal SubunitQizhi Cui, Robert K.-Z. Tan, Stephen C. Harvey, David A. Case. mmas, 5(4):1248-1263, 2006. [doi]

A comparison of quantum chemical models for calculating NMR shielding parameters in peptides: Mixed basis set and ONIOM methods combined with a complete basis set extrapolationSeongho Moon, David A. Case. jcc, 27(7):825-836, 2006. [doi]

2005

2004

2002

Effective Born radii in the generalized Born approximation: The importance of being perfectAlexey Onufriev, David A. Case, Donald Bashford. jcc, 23(14):1297-1304, 2002. [doi]

1993

Computer Simulations of Protein Dynamics and ThermodynamicsDavid A. Case. Computer, 26(10):47-57, 1993.

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