John L. Klepeis, Ph.D.

Affiliations: 
Princeton University, Princeton, NJ 
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"John Klepeis"
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SNBCP

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Christodoulos A. Floudas grad student 2002 Princeton
 (Global optimization in protein folding.)
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Publications

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Piana S, Klepeis JL, Shaw DE. (2014) Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations. Current Opinion in Structural Biology. 24: 98-105
Chow E, Klepeis JL, Rendleman CA, et al. (2012) New technologies for molecular dynamics simulations Comprehensive Biophysics. 9: 86-104
Lindorff-Larsen K, Piana S, Palmo K, et al. (2010) Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins. 78: 1950-8
Klepeis JL, Lindorff-Larsen K, Dror RO, et al. (2009) Long-timescale molecular dynamics simulations of protein structure and function. Current Opinion in Structural Biology. 19: 120-7
Shaw DE, Dror RO, Salmon JK, et al. (2009) Millisecond-scale molecular dynamics simulations on Anton Proceedings of the Conference On High Performance Computing Networking, Storage and Analysis, Sc '09
Maragakis P, Lindorff-Larsen K, Eastwood MP, et al. (2008) Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins. The Journal of Physical Chemistry. B. 112: 6155-8
Shaw DE, Deneroff MM, Dror RO, et al. (2008) Anton, a special-purpose machine for molecular dynamics simulation Communications of the Acm. 51: 91-97
Tu T, Rendleman CA, Borhani DW, et al. (2008) A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories 2008 Sc - International Conference For High Performance Computing, Networking, Storage and Analysis, Sc 2008
Larson RH, Salmon JK, Dror RO, et al. (2008) High-throughput pairwise point interactions in anton, a specialized machine for molecular dynamics simulation Proceedings - International Symposium On High-Performance Computer Architecture. 331-342
Arkin IT, Xu H, Jensen MØ, et al. (2007) Mechanism of Na+/H+ antiporting. Science (New York, N.Y.). 317: 799-803
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