David A. Case

According to our database, David A. Case authored at least 25 papers between 1993 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

X-ray Crystallography Module in MD Simulation Program Amber 2023. Refining the Models of Protein Crystals.

Oleg Mikhailovskii, Sergei A. Izmailov, Yi Xue, David A. Case, Nikolai R. Skrynnikov

J. Chem. Inf. Model., January, 2024

2023

AmberTools.

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.

J. Chem. Inf. Model., October, 2023

2018

GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features.

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

J. Chem. Inf. Model., 2018

NGLview-interactive molecular graphics for Jupyter notebooks.

Hai Nguyen, David A. Case, Alexander S. Rose

Bioinform., 2018

2017

Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong

J. Comput. Aided Mol. Des., 2017

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong

J. Comput. Aided Mol. Des., 2017

2016

The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP.

Yuan Hu, Brad Sherborne, Tai-Sung Lee, David A. Case, Darrin M. York, Zhuyan Guo

J. Comput. Aided Mol. Des., 2016

2015

DOCK 6: Impact of new features and current docking performance.

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

J. Comput. Chem., 2015

2012

Energetic Selection of Topology in Ferredoxins.

J. Dongun Kim, Agustina Rodriguez-Granillo, David A. Case, Vikas Nanda, Paul G. Falkowski

PLoS Comput. Biol., 2012

Evaluation of DOCK 6 as a pose generation and database enrichment tool.

Scott R. Brozell, Sudipto Mukherjee, Trent E. Balius, Daniel R. Roe, David A. Case, Robert C. Rizzo

J. Comput. Aided Mol. Des., 2012

2011

Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformations.

Thomas Steinbrecher, InSuk Joung, David A. Case

J. Comput. Chem., 2011

A Grid-enabled web portal for NMR structure refinement with AMBER.

Ivano Bertini, David A. Case, Lucio Ferella, Andrea Giachetti, Antonio Rosato

Bioinform., 2011

2008

The implementation of a fast and accurate QM/MM potential method in Amber.

Ross C. Walker, Michael F. Crowley, David A. Case

J. Comput. Chem., 2008

2006

Low-Resolution Molecular Dynamics Simulations of the 30S Ribosomal Subunit.

Qizhi Cui, Robert K.-Z. Tan, Stephen C. Harvey, David A. Case

Multiscale Model. Simul., 2006

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.

Seongho Moon, David A. Case

J. Comput. Chem., 2006

Second derivatives in generalized Born theory.

Russell A. Brown, David A. Case

J. Comput. Chem., 2006

2005

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.

Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, David A. Case

J. Comput. Chem., 2005

The Amber biomolecular simulation programs.

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

J. Comput. Chem., 2005

Invited Talk: Macromolecular Simulations Using Continuum Solvent Models.

David A. Case

Proceedings of the German Conference on Bioinformatics (GCB 2005), Hamburg, 2005

2004

Development and testing of a general amber force field.

Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, David A. Case

J. Comput. Chem., 2004

Constant pH molecular dynamics in generalized Born implicit solvent.

John Mongan, David A. Case, James Andrew McCammon

J. Comput. Chem., 2004

Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.

Holger Gohlke, David A. Case

J. Comput. Chem., 2004

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures.

Michael Feig, Alexey Onufriev, Michael S. Lee, Wonpil Im, David A. Case, Charles L. Brooks III

J. Comput. Chem., 2004

2002

Effective Born radii in the generalized Born approximation: The importance of being perfect.

Alexey Onufriev, David A. Case, Donald Bashford

J. Comput. Chem., 2002

1993

Computer Simulations of Protein Dynamics and Thermodynamics.

David A. Case

Computer, 1993