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101 results
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Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase.
Mondal J, Friesner RA, Berne BJ. Mondal J, et al. Among authors: berne bj. J Chem Theory Comput. 2014 Dec 9;10(12):5696-5705. doi: 10.1021/ct500584n. Epub 2014 Nov 13. J Chem Theory Comput. 2014. PMID: 25516727 Free PMC article.
Efficient sampling of puckering states of monosaccharides through replica exchange with solute tempering and bond softening.
Wang L, Berne BJ. Wang L, et al. Among authors: berne bj. J Chem Phys. 2018 Aug 21;149(7):072306. doi: 10.1063/1.5024389. J Chem Phys. 2018. PMID: 30134707
How wet should be the reaction coordinate for ligand unbinding?
Tiwary P, Berne BJ. Tiwary P, et al. Among authors: berne bj. J Chem Phys. 2016 Aug 7;145(5):054113. doi: 10.1063/1.4959969. J Chem Phys. 2016. PMID: 27497545 Free PMC article.
Prediction of Protein-Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations.
Clark AJ, Tiwary P, Borrelli K, Feng S, Miller EB, Abel R, Friesner RA, Berne BJ. Clark AJ, et al. Among authors: berne bj. J Chem Theory Comput. 2016 Jun 14;12(6):2990-8. doi: 10.1021/acs.jctc.6b00201. Epub 2016 May 13. J Chem Theory Comput. 2016. PMID: 27145262
Kramers turnover: From energy diffusion to spatial diffusion using metadynamics.
Tiwary P, Berne BJ. Tiwary P, et al. Among authors: berne bj. J Chem Phys. 2016 Apr 7;144(13):134103. doi: 10.1063/1.4944577. J Chem Phys. 2016. PMID: 27059558 Free PMC article.
How a Kinase Inhibitor Withstands Gatekeeper Residue Mutations.
Mondal J, Tiwary P, Berne BJ. Mondal J, et al. Among authors: berne bj. J Am Chem Soc. 2016 Apr 6;138(13):4608-15. doi: 10.1021/jacs.6b01232. Epub 2016 Mar 22. J Am Chem Soc. 2016. PMID: 26954686
Efficient Simulation Method for Polarizable Protein Force Fields:‚ÄČ Application to the Simulation of BPTI in Liquid Water.
Harder E, Kim B, Friesner RA, Berne BJ. Harder E, et al. Among authors: berne bj. J Chem Theory Comput. 2005 Jan;1(1):169-80. doi: 10.1021/ct049914s. J Chem Theory Comput. 2005. PMID: 26641127
A displaced-solvent functional analysis of model hydrophobic enclosures.
Abel R, Wang L, Friesner RA, Berne BJ. Abel R, et al. Among authors: berne bj. J Chem Theory Comput. 2010 Aug 20;6(9):2924-2934. doi: 10.1021/ct100215c. J Chem Theory Comput. 2010. PMID: 21135914 Free PMC article.
Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances.
Morrone JA, Markland TE, Ceriotti M, Berne BJ. Morrone JA, et al. Among authors: berne bj. J Chem Phys. 2011 Jan 7;134(1):014103. doi: 10.1063/1.3518369. J Chem Phys. 2011. PMID: 21218993
Molecular Dynamics with Multiple Time Scales: How to Avoid Pitfalls.
Morrone JA, Zhou R, Berne BJ. Morrone JA, et al. Among authors: berne bj. J Chem Theory Comput. 2010 Jun 8;6(6):1798-804. doi: 10.1021/ct100054k. Epub 2010 May 19. J Chem Theory Comput. 2010. PMID: 26615840
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