David A. Case

Publication Activity (10 Years)

Years Active: 1993-2024
Publications (10 Years): 8

Top Topics

Molecular Dynamics

Scientific Data

Chest Radiographs

Top Venues

J. Chem. Inf. Model.

J. Comput. Aided Mol. Des.

J. Comput. Chem.

Publications

Oleg Mikhailovskii, Sergei A. Izmailov, Yi Xue, David A. Case, Nikolai R. Skrynnikov
X-ray Crystallography Module in MD Simulation Program Amber 2023. Refining the Models of Protein Crystals. J. Chem. Inf. Model. 64 (1) (2024)
David A. Case, Hasan Metin Aktulga, Kellon Belfon, David S. Cerutti, G. Andrés Cisneros, Vinícius Wilian D. Cruzeiro, Negin Forouzesh, Timothy J. Giese, Andreas W. Götz, Holger Gohlke, Saeed Izadi, Koushik Kasavajhala, Mehmet Cagri Kaymak, Edward King, Tom Kurtzman, Tai-Sung Lee, Pengfei Li, Jian Liu, Tyler Luchko, Ray Luo, Madushanka Manathunga, Matías R. Machado, Hai Minh Nguyen, Kurt A. O'Hearn, Alexey V. Onufriev, Feng Pan, Sergio Pantano, Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo, Akhil Shajan, Jason M. Swails, Junmei Wang, Haixin Wei, Xiongwu Wu, Yongxian Wu, Shi Zhang, Shiji Zhao, Qiang Zhu, Thomas E. Cheatham, Daniel R. Roe, Adrian E. Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz Jr.
AmberTools. J. Chem. Inf. Model. 63 (20) (2023)
Hai Nguyen, David A. Case, Alexander S. Rose
NGLview-interactive molecular graphics for Jupyter notebooks. Bioinform. 34 (7) (2018)
Tai-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
GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features. J. Chem. Inf. Model. 58 (10) (2018)
Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong
Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J. Comput. Aided Mol. Des. 31 (8) (2017)
Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong
Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J. Comput. Aided Mol. Des. 31 (1) (2017)
Yuan Hu, Brad Sherborne, Tai-Sung Lee, David A. Case, Darrin M. York, Zhuyan Guo
The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP. J. Comput. Aided Mol. Des. 30 (7) (2016)
William J. Allen, Trent E. Balius, Sudipto Mukherjee, Scott R. Brozell, Demetri Moustakas, P. Therese Lang, David A. Case, Irwin D. Kuntz, Robert C. Rizzo
DOCK 6: Impact of new features and current docking performance. J. Comput. Chem. 36 (15) (2015)
Scott R. Brozell, Sudipto Mukherjee, Trent E. Balius, Daniel R. Roe, David A. Case, Robert C. Rizzo
Evaluation of DOCK 6 as a pose generation and database enrichment tool. J. Comput. Aided Mol. Des. 26 (6) (2012)
J. Dongun Kim, Agustina Rodriguez-Granillo, David A. Case, Vikas Nanda, Paul G. Falkowski
Energetic Selection of Topology in Ferredoxins. PLoS Comput. Biol. 8 (4) (2012)
Thomas Steinbrecher, InSuk Joung, David A. Case
Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformations. J. Comput. Chem. 32 (15) (2011)
Ivano Bertini, David A. Case, Lucio Ferella, Andrea Giachetti, Antonio Rosato
A Grid-enabled web portal for NMR structure refinement with AMBER. Bioinform. 27 (17) (2011)
Ross C. Walker, Michael F. Crowley, David A. Case
The implementation of a fast and accurate QM/MM potential method in Amber. J. Comput. Chem. 29 (7) (2008)
Qizhi Cui, Robert K.-Z. Tan, Stephen C. Harvey, David A. Case
Low-Resolution Molecular Dynamics Simulations of the 30S Ribosomal Subunit. Multiscale Model. Simul. 5 (4) (2006)
Russell A. Brown, David A. Case
Second derivatives in generalized Born theory. J. Comput. Chem. 27 (14) (2006)
Seongho Moon, David A. Case
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 extrapolation. J. Comput. Chem. 27 (7) (2006)
David A. Case, Thomas E. Cheatham III, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M. Merz Jr., Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods
The Amber biomolecular simulation programs. J. Comput. Chem. 26 (16) (2005)
Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, David A. Case
Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, and David A. Case, "Development and testing of a general amber force field" Journal of Computational Chemistry(2004) 25(9) 1157-1174. J. Comput. Chem. 26 (1) (2005)
David A. Case
Invited Talk: Macromolecular Simulations Using Continuum Solvent Models. German Conference on Bioinformatics (2005)
Michael Feig, Alexey Onufriev, Michael S. Lee, Wonpil Im, David A. Case, Charles L. Brooks III
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J. Comput. Chem. 25 (2) (2004)
Holger Gohlke, David A. Case
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. J. Comput. Chem. 25 (2) (2004)
John Mongan, David A. Case, J. Andrew McCammon
Constant pH molecular dynamics in generalized Born implicit solvent. J. Comput. Chem. 25 (16) (2004)
Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, David A. Case
Development and testing of a general amber force field. J. Comput. Chem. 25 (9) (2004)
Alexey Onufriev, David A. Case, Donald Bashford
Effective Born radii in the generalized Born approximation: The importance of being perfect. J. Comput. Chem. 23 (14) (2002)
David A. Case
Computer Simulations of Protein Dynamics and Thermodynamics. Computer 26 (10) (1993)