Cui Q - Search Results

1

Establishing effective simulation protocols for beta- and alpha/beta-peptides. III. Molecular mechanical model for acyclic beta-amino acids.

Zhu X, Koenig P, Hoffmann M, Yethiraj A, Cui Q. Zhu X, et al. Among authors: cui q. J Comput Chem. 2010 Jul 30;31(10):2063-77. doi: 10.1002/jcc.21493. J Comput Chem. 2010. PMID: 20175215

2

Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps.

König PH, Ghosh N, Hoffmann M, Elstner M, Tajkhorshid E, Frauenheim T, Cui Q. König PH, et al. Among authors: cui q. J Phys Chem A. 2006 Jan 19;110(2):548-63. doi: 10.1021/jp052328q. J Phys Chem A. 2006. PMID: 16405327 Free PMC article.

3

Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes.

Riccardi D, Schaefer P, Yang Y, Yu H, Ghosh N, Prat-Resina X, König P, Li G, Xu D, Guo H, Elstner M, Cui Q. Riccardi D, et al. Among authors: cui q. J Phys Chem B. 2006 Apr 6;110(13):6458-69. doi: 10.1021/jp056361o. J Phys Chem B. 2006. PMID: 16570942

4

A finite element framework for studying the mechanical response of macromolecules: application to the gating of the mechanosensitive channel MscL.

Tang Y, Cao G, Chen X, Yoo J, Yethiraj A, Cui Q. Tang Y, et al. Among authors: cui q. Biophys J. 2006 Aug 15;91(4):1248-63. doi: 10.1529/biophysj.106.085985. Epub 2006 May 26. Biophys J. 2006. PMID: 16731564 Free PMC article.

5

A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method.

König PH, Hoffmann M, Frauenheim T, Cui Q. König PH, et al. Among authors: cui q. J Phys Chem B. 2005 May 12;109(18):9082-95. doi: 10.1021/jp0442347. J Phys Chem B. 2005. PMID: 16852081

6

pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.

Riccardi D, Schaefer P, Cui Q. Riccardi D, et al. Among authors: cui q. J Phys Chem B. 2005 Sep 22;109(37):17715-33. doi: 10.1021/jp0517192. J Phys Chem B. 2005. PMID: 16853267

7

The use of a generalized born model for the analysis of protein conformational transitions: a comparative study with explicit solvent simulations for chemotaxis Y protein (CheY).

Formaneck MS, Cui Q. Formaneck MS, et al. Among authors: cui q. J Comput Chem. 2006 Dec;27(16):1923-43. doi: 10.1002/jcc.20489. J Comput Chem. 2006. PMID: 17019722

8

pKa analysis for the zinc-bound water in human carbonic anhydrase II: Benchmark for "multiscale" QM/MM simulations and mechanistic implications.

Riccardi D, Cui Q. Riccardi D, et al. Among authors: cui q. J Phys Chem A. 2007 Jul 5;111(26):5703-11. doi: 10.1021/jp070699w. Epub 2007 May 17. J Phys Chem A. 2007. PMID: 17506534

9

Gating mechanisms of mechanosensitive channels of large conductance, II: systematic study of conformational transitions.

Tang Y, Yoo J, Yethiraj A, Cui Q, Chen X. Tang Y, et al. Among authors: cui q. Biophys J. 2008 Jul;95(2):581-96. doi: 10.1529/biophysj.107.128496. Epub 2008 Apr 4. Biophys J. 2008. PMID: 18390625 Free PMC article.

10

Gating mechanisms of mechanosensitive channels of large conductance, I: a continuum mechanics-based hierarchical framework.

Chen X, Cui Q, Tang Y, Yoo J, Yethiraj A. Chen X, et al. Among authors: cui q. Biophys J. 2008 Jul;95(2):563-80. doi: 10.1529/biophysj.107.128488. Epub 2008 Apr 4. Biophys J. 2008. PMID: 18390626 Free PMC article.

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