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Scalable molecular dynamics with NAMD.
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K. Phillips JC, et al. J Comput Chem. 2005 Dec;26(16):1781-802. doi: 10.1002/jcc.20289. J Comput Chem. 2005. PMID: 16222654 Free PMC article.
Quantum dynamics of the femtosecond photoisomerization of retinal in bacteriorhodopsin.
Ben-Nun M, Molnar F, Lu H, Phillips JC, Martínez TJ, Schulten K. Ben-Nun M, et al. Among authors: phillips jc. Faraday Discuss. 1998;(110):447-62; discussion 477-520. doi: 10.1039/a801310a. Faraday Discuss. 1998. PMID: 10822594
Large scale simulation of protein mechanics and function.
Tajkhorshid E, Aksimentiev A, Balabin I, Gao M, Isralewitz B, Phillips JC, Zhu F, Schulten K. Tajkhorshid E, et al. Among authors: phillips jc. Adv Protein Chem. 2003;66:195-247. doi: 10.1016/s0065-3233(03)66006-7. Adv Protein Chem. 2003. PMID: 14631820 Review. No abstract available.
Molecular dynamics simulations of discoidal bilayers assembled from truncated human lipoproteins.
Shih AY, Denisov IG, Phillips JC, Sligar SG, Schulten K. Shih AY, et al. Among authors: phillips jc. Biophys J. 2005 Jan;88(1):548-56. doi: 10.1529/biophysj.104.046896. Epub 2004 Nov 8. Biophys J. 2005. PMID: 15533924 Free PMC article.
Accelerating molecular modeling applications with graphics processors.
Stone JE, Phillips JC, Freddolino PL, Hardy DJ, Trabuco LG, Schulten K. Stone JE, et al. Among authors: phillips jc. J Comput Chem. 2007 Dec;28(16):2618-40. doi: 10.1002/jcc.20829. J Comput Chem. 2007. PMID: 17894371
High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD.
Jiang W, Hardy DJ, Phillips JC, Mackerell AD Jr, Schulten K, Roux B. Jiang W, et al. Among authors: phillips jc. J Phys Chem Lett. 2011;2(2):87-92. doi: 10.1021/jz101461d. J Phys Chem Lett. 2011. PMID: 21572567 Free PMC article.
Parallel Generalized Born Implicit Solvent Calculations with NAMD.
Tanner DE, Chan KY, Phillips JC, Schulten K. Tanner DE, et al. Among authors: phillips jc. J Chem Theory Comput. 2011 Nov 8;7(11):3635-3642. doi: 10.1021/ct200563j. J Chem Theory Comput. 2011. PMID: 22121340 Free PMC article.
GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations.
Tanner DE, Phillips JC, Schulten K. Tanner DE, et al. Among authors: phillips jc. J Chem Theory Comput. 2012 Jul 10;8(7):2521-2530. doi: 10.1021/ct3003089. Epub 2012 Jun 15. J Chem Theory Comput. 2012. PMID: 23049488 Free PMC article.
Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD.
Jiang W, Phillips JC, Huang L, Fajer M, Meng Y, Gumbart JC, Luo Y, Schulten K, Roux B. Jiang W, et al. Among authors: phillips jc. Comput Phys Commun. 2014 Mar;185(3):908-916. doi: 10.1016/j.cpc.2013.12.014. Comput Phys Commun. 2014. PMID: 24944348 Free PMC article.
Multilevel summation method for electrostatic force evaluation.
Hardy DJ, Wu Z, Phillips JC, Stone JE, Skeel RD, Schulten K. Hardy DJ, et al. Among authors: phillips jc. J Chem Theory Comput. 2015 Feb 10;11(2):766-79. doi: 10.1021/ct5009075. J Chem Theory Comput. 2015. PMID: 25691833 Free PMC article.
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