David A. Case

26 papers Journal 25Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
Recent Developments in Amber Biomolecular Simulations.
J. Chem. Inf. Model.
David A. Case, David S. Cerutti, Vinícius Wilian D. Cruzeiro, Thomas A. Darden, Robert E. Duke, Mahdieh Ghazimirsaeed, George M. Giambasu, Timothy J. Giese, Andreas W. Götz, Julie A. Harris, Koushik Kasavajhala, Tai-Sung Lee, Zhen Li, Charles Lin, Jian Liu, Yinglong Miao, Romelia Salomón-Ferrer, Jana Shen, Ryan Snyder, Jason M. Swails, Ross C. Walker, Jinan Wang, Xiongwu Wu, Jinzhe Zeng, Thomas E. Cheatham III, Daniel R. Roe, Adrian E. Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz Jr.
2024 J jnl
X-ray Crystallography Module in MD Simulation Program Amber 2023. Refining the Models of Protein Crystals.
J. Chem. Inf. Model.
Oleg Mikhailovskii, Sergei A. Izmailov, Yi Xue, David A. Case, Nikolai R. Skrynnikov
2023 J jnl
AmberTools.
J. Chem. Inf. Model.
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.
2018 J jnl
GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features.
J. Chem. Inf. Model.
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
2018 J jnl
NGLview-interactive molecular graphics for Jupyter notebooks.
Bioinform.
Hai Nguyen, David A. Case, Alexander S. Rose
2017 J jnl
Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.
J. Comput. Aided Mol. Des.
Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong
2017 J jnl
Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.
J. Comput. Aided Mol. Des.
Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong
2016 J jnl
The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP.
J. Comput. Aided Mol. Des.
Yuan Hu, Brad Sherborne, Tai-Sung Lee, David A. Case, Darrin M. York, Zhuyan Guo
2015 J jnl
DOCK 6: Impact of new features and current docking performance.
J. Comput. Chem.
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
2012 J jnl
Energetic Selection of Topology in Ferredoxins.
PLoS Comput. Biol.
J. Dongun Kim, Agustina Rodriguez-Granillo, David A. Case, Vikas Nanda, Paul G. Falkowski
2012 J jnl
Evaluation of DOCK 6 as a pose generation and database enrichment tool.
J. Comput. Aided Mol. Des.
Scott R. Brozell, Sudipto Mukherjee, Trent E. Balius, Daniel R. Roe, David A. Case, Robert C. Rizzo
2011 J jnl
A Grid-enabled web portal for NMR structure refinement with AMBER.
Bioinform.
Ivano Bertini, David A. Case, Lucio Ferella, Andrea Giachetti, Antonio Rosato
2011 J jnl
Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformations.
J. Comput. Chem.
Thomas Steinbrecher, InSuk Joung, David A. Case
2008 J jnl
The implementation of a fast and accurate QM/MM potential method in Amber.
J. Comput. Chem.
Ross C. Walker, Michael F. Crowley, David A. Case
2006 J jnl
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.
Seongho Moon, David A. Case
2006 J jnl
Low-Resolution Molecular Dynamics Simulations of the 30S Ribosomal Subunit.
Multiscale Model. Simul.
Qizhi Cui, Robert K.-Z. Tan, Stephen C. Harvey, David A. Case
2006 J jnl
Second derivatives in generalized Born theory.
J. Comput. Chem.
Russell A. Brown, David A. Case
2005 — conf
Invited Talk: Macromolecular Simulations Using Continuum Solvent Models.
German Conference on Bioinformatics
David A. Case
2005 J jnl
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.
Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, David A. Case
2005 J jnl
The Amber biomolecular simulation programs.
J. Comput. Chem.
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
2004 J jnl
Constant pH molecular dynamics in generalized Born implicit solvent.
J. Comput. Chem.
John Mongan, David A. Case, James Andrew McCammon
2004 J jnl
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.
J. Comput. Chem.
Holger Gohlke, David A. Case
2004 J jnl
Development and testing of a general amber force field.
J. Comput. Chem.
Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, David A. Case
2004 J jnl
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures.
J. Comput. Chem.
Michael Feig, Alexey Onufriev, Michael S. Lee, Wonpil Im, David A. Case, Charles L. Brooks III
2002 J jnl
Effective Born radii in the generalized Born approximation: The importance of being perfect.
J. Comput. Chem.
Alexey Onufriev, David A. Case, Donald Bashford
1993 J jnl
Computer Simulations of Protein Dynamics and Thermodynamics.
Computer
David A. Case