Cui Q - Search Results

1

Establishing effective simulation protocols for beta- and alpha/beta-peptides. II. Molecular mechanical (MM) model for a cyclic beta-residue.

Zhu X, Koenig P, Gellman SH, Yethiraj A, Cui Q. Zhu X, et al. Among authors: cui q. J Phys Chem B. 2008 May 1;112(17):5439-48. doi: 10.1021/jp077601y. Epub 2008 Apr 11. J Phys Chem B. 2008. PMID: 18402479

2

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

3

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.

4

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

5

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

6

TiIV-mediated reactions between primary amines and secondary carboxamides: amidine formation versus transamidation.

Kissounko DA, Hoerter JM, Guzei IA, Cui Q, Gellman SH, Stahl SS. Kissounko DA, et al. Among authors: cui q. J Am Chem Soc. 2007 Feb 14;129(6):1776-83. doi: 10.1021/ja0650293. J Am Chem Soc. 2007. PMID: 17284008

7

Antibiotic binding to dizinc beta-lactamase L1 from Stenotrophomonas maltophilia: SCC-DFTB/CHARMM and DFT studies.

Xu D, Guo H, Cui Q. Xu D, et al. Among authors: cui q. J Phys Chem A. 2007 Jul 5;111(26):5630-6. doi: 10.1021/jp068746s. Epub 2007 Mar 3. J Phys Chem A. 2007. PMID: 17388313

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

Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction.

Yang Y, Yu H, York D, Cui Q, Elstner M. Yang Y, et al. Among authors: cui q. J Phys Chem A. 2007 Oct 25;111(42):10861-73. doi: 10.1021/jp074167r. Epub 2007 Oct 3. J Phys Chem A. 2007. PMID: 17914769

10

Discovery and mechanistic study of Al(III)-catalyzed transamidation of tertiary amides.

Hoerter JM, Otte KM, Gellman SH, Cui Q, Stahl SS. Hoerter JM, et al. Among authors: cui q. J Am Chem Soc. 2008 Jan 16;130(2):647-54. doi: 10.1021/ja0762994. Epub 2007 Dec 20. J Am Chem Soc. 2008. PMID: 18092780

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