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Transferable Neural Networks for Enhanced Sampling of Protein Dynamics.
Sultan MM, Wayment-Steele HK, Pande VS. Sultan MM, et al. Among authors: pande vs. J Chem Theory Comput. 2018 Apr 10;14(4):1887-1894. doi: 10.1021/acs.jctc.8b00025. Epub 2018 Mar 19. J Chem Theory Comput. 2018. PMID: 29529369
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.
Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y, Jo S, Pande VS, Case DA, Brooks CL 3rd, MacKerell AD Jr, Klauda JB, Im W. Lee J, et al. Among authors: pande vs. J Chem Theory Comput. 2016 Jan 12;12(1):405-13. doi: 10.1021/acs.jctc.5b00935. Epub 2015 Dec 3. J Chem Theory Comput. 2016. PMID: 26631602 Free PMC article.
Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics.
McGibbon RT, Pande VS. McGibbon RT, et al. Among authors: pande vs. J Chem Theory Comput. 2013 Jul 9;9(7):2900-6. doi: 10.1021/ct400132h. Epub 2013 Jun 6. J Chem Theory Comput. 2013. PMID: 26583974
Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9.
Schwantes CR, Pande VS. Schwantes CR, et al. Among authors: pande vs. J Chem Theory Comput. 2013 Apr 9;9(4):2000-2009. doi: 10.1021/ct300878a. J Chem Theory Comput. 2013. PMID: 23750122 Free PMC article.
MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale.
Beauchamp KA, Bowman GR, Lane TJ, Maibaum L, Haque IS, Pande VS. Beauchamp KA, et al. Among authors: pande vs. J Chem Theory Comput. 2011 Oct 11;7(10):3412-3419. doi: 10.1021/ct200463m. J Chem Theory Comput. 2011. PMID: 22125474 Free PMC article.
Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics.
Prinz JH, Chodera JD, Pande VS, Swope WC, Smith JC, NoƩ F. Prinz JH, et al. Among authors: pande vs. J Chem Phys. 2011 Jun 28;134(24):244108. doi: 10.1063/1.3592153. J Chem Phys. 2011. PMID: 21721613 Free PMC article.
Markov state model reveals folding and functional dynamics in ultra-long MD trajectories.
Lane TJ, Bowman GR, Beauchamp K, Voelz VA, Pande VS. Lane TJ, et al. Among authors: pande vs. J Am Chem Soc. 2011 Nov 16;133(45):18413-9. doi: 10.1021/ja207470h. Epub 2011 Oct 26. J Am Chem Soc. 2011. PMID: 21988563 Free PMC article.
tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective Variables.
M Sultan M, Pande VS. M Sultan M, et al. Among authors: pande vs. J Chem Theory Comput. 2017 Jun 13;13(6):2440-2447. doi: 10.1021/acs.jctc.7b00182. Epub 2017 May 9. J Chem Theory Comput. 2017. PMID: 28383914
Training and Validation of a Liquid-Crystalline Phospholipid Bilayer Force Field.
McKiernan KA, Wang LP, Pande VS. McKiernan KA, et al. Among authors: pande vs. J Chem Theory Comput. 2016 Dec 13;12(12):5960-5967. doi: 10.1021/acs.jctc.6b00801. Epub 2016 Nov 21. J Chem Theory Comput. 2016. PMID: 27786477
Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways.
Wang LP, McGibbon RT, Pande VS, Martinez TJ. Wang LP, et al. Among authors: pande vs. J Chem Theory Comput. 2016 Feb 9;12(2):638-49. doi: 10.1021/acs.jctc.5b00830. Epub 2016 Jan 19. J Chem Theory Comput. 2016. PMID: 26683346
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