Duan Y - Search Results

1

PyRESP: A Program for Electrostatic Parameterizations of Additive and Induced Dipole Polarizable Force Fields.

Zhao S, Wei H, Cieplak P, Duan Y, Luo R. Zhao S, et al. Among authors: duan y. J Chem Theory Comput. 2022 Jun 14;18(6):3654-3670. doi: 10.1021/acs.jctc.2c00230. Epub 2022 May 10. J Chem Theory Comput. 2022. PMID: 35537209 Free PMC article.

2

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.

Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE 3rd. Kollman PA, et al. Among authors: duan y. Acc Chem Res. 2000 Dec;33(12):889-97. doi: 10.1021/ar000033j. Acc Chem Res. 2000. PMID: 11123888

3

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P. Duan Y, et al. J Comput Chem. 2003 Dec;24(16):1999-2012. doi: 10.1002/jcc.10349. J Comput Chem. 2003. PMID: 14531054

4

Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides.

Wang ZX, Zhang W, Wu C, Lei H, Cieplak P, Duan Y. Wang ZX, et al. Among authors: duan y. J Comput Chem. 2006 Apr 30;27(6):781-90. doi: 10.1002/jcc.20386. J Comput Chem. 2006. PMID: 16526038 Free PMC article.

5

New-generation amber united-atom force field.

Yang L, Tan CH, Hsieh MJ, Wang J, Duan Y, Cieplak P, Caldwell J, Kollman PA, Luo R. Yang L, et al. Among authors: duan y. J Phys Chem B. 2006 Jul 6;110(26):13166-76. doi: 10.1021/jp060163v. J Phys Chem B. 2006. PMID: 16805629

6

Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability.

Wang J, Cieplak P, Li J, Hou T, Luo R, Duan Y. Wang J, et al. Among authors: duan y. J Phys Chem B. 2011 Mar 31;115(12):3091-9. doi: 10.1021/jp112133g. Epub 2011 Mar 10. J Phys Chem B. 2011. PMID: 21391553 Free PMC article.

7

Development of polarizable models for molecular mechanical calculations II: induced dipole models significantly improve accuracy of intermolecular interaction energies.

Wang J, Cieplak P, Li J, Wang J, Cai Q, Hsieh M, Lei H, Luo R, Duan Y. Wang J, et al. Among authors: duan y. J Phys Chem B. 2011 Mar 31;115(12):3100-11. doi: 10.1021/jp1121382. Epub 2011 Mar 10. J Phys Chem B. 2011. PMID: 21391583 Free PMC article.

8

Polarization effects in molecular mechanical force fields.

Cieplak P, Dupradeau FY, Duan Y, Wang J. Cieplak P, et al. Among authors: duan y. J Phys Condens Matter. 2009 Aug 19;21(33):333102. doi: 10.1088/0953-8984/21/33/333102. Epub 2009 Jul 24. J Phys Condens Matter. 2009. PMID: 21828594 Free PMC article.

9

Development of polarizable models for molecular mechanical calculations. 4. van der Waals parametrization.

Wang J, Cieplak P, Li J, Cai Q, Hsieh MJ, Luo R, Duan Y. Wang J, et al. Among authors: duan y. J Phys Chem B. 2012 Jun 21;116(24):7088-101. doi: 10.1021/jp3019759. Epub 2012 Jun 6. J Phys Chem B. 2012. PMID: 22612331 Free PMC article.

10

Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes.

Wang J, Cieplak P, Cai Q, Hsieh MJ, Wang J, Duan Y, Luo R. Wang J, et al. Among authors: duan y. J Phys Chem B. 2012 Jul 19;116(28):7999-8008. doi: 10.1021/jp212117d. Epub 2012 Jul 5. J Phys Chem B. 2012. PMID: 22712654 Free PMC article.

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