| Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models PA Kollman, I Massova, C Reyes, B Kuhn, S Huo, L Chong, M Lee, T Lee, ... Accounts of chemical research 33 (12), 889-897, 2000 | 4961 | 2000 |
| A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations Y Duan, C Wu, S Chowdhury, MC Lee, G Xiong, W Zhang, R Yang, ... Journal of computational chemistry 24 (16), 1999-2012, 2003 | 4901 | 2003 |
| Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution Y Duan, PA Kollman Science 282 (5389), 740-744, 1998 | 1754 | 1998 |
| Polarization effects in molecular mechanical force fields P Cieplak, FY Dupradeau, Y Duan, J Wang Journal of Physics: Condensed Matter 21 (33), 333102, 2009 | 380 | 2009 |
| Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model MC Lee, Y Duan Proteins: Structure, Function, and Bioinformatics 55 (3), 620-634, 2004 | 311 | 2004 |
| Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7 LT Chong, Y Duan, L Wang, I Massova, PA Kollman Proceedings of the National Academy of Sciences 96 (25), 14330-14335, 1999 | 305 | 1999 |
| Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations H Lei, C Wu, H Liu, Y Duan Proceedings of the National Academy of Sciences 104 (12), 4925-4930, 2007 | 268 | 2007 |
| New-generation amber united-atom force field L Yang, C Tan, MJ Hsieh, J Wang, Y Duan, P Cieplak, J Caldwell, ... The journal of physical chemistry B 110 (26), 13166-13176, 2006 | 238 | 2006 |
| Use of MM‐PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece MR Lee, Y Duan, PA Kollman Proteins: Structure, Function, and Bioinformatics 39 (4), 309-316, 2000 | 236 | 2000 |
| The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation Y Duan, L Wang, PA Kollman Proceedings of the National Academy of Sciences 95 (17), 9897-9902, 1998 | 226 | 1998 |
| Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides ZX Wang, W Zhang, C Wu, H Lei, P Cieplak, Y Duan Journal of computational chemistry 27 (6), 781-790, 2006 | 218 | 2006 |
| Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution S Chowdhury, MC Lee, G Xiong, Y Duan Journal of molecular biology 327 (3), 711-717, 2003 | 201 | 2003 |
| Dual binding modes of Congo red to amyloid protofibril surface observed in molecular dynamics simulations C Wu, Z Wang, H Lei, W Zhang, Y Duan Journal of the American Chemical Society 129 (5), 1225-1232, 2007 | 187 | 2007 |
| The binding of thioflavin T and its neutral analog BTA-1 to protofibrils of the Alzheimer’s disease Aβ16–22 peptide probed by molecular dynamics simulations C Wu, Z Wang, H Lei, Y Duan, MT Bowers, JE Shea Journal of molecular biology 384 (3), 718-729, 2008 | 176 | 2008 |
| Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability J Wang, P Cieplak, J Li, T Hou, R Luo, Y Duan The Journal of Physical Chemistry B 115 (12), 3091-3099, 2011 | 168 | 2011 |
| Development of polarizable models for molecular mechanical calculations II: induced dipole models significantly improve accuracy of intermolecular interaction energies J Wang, P Cieplak, J Li, J Wang, Q Cai, MJ Hsieh, H Lei, R Luo, Y Duan The journal of physical chemistry B 115 (12), 3100-3111, 2011 | 146 | 2011 |
| Improved sampling methods for molecular simulation H Lei, Y Duan Current opinion in structural biology 17 (2), 187-191, 2007 | 143 | 2007 |
| Convergence of replica exchange molecular dynamics W Zhang, C Wu, Y Duan The Journal of chemical physics 123 (15), 2005 | 143 | 2005 |
| Solvation effects on alanine dipeptide: A MP2/cc‐pVTZ//MP2/6‐31G** study of (Φ, Ψ) energy maps and conformers in the gas phase, ether, and water ZX Wang, Y Duan Journal of computational chemistry 25 (14), 1699-1716, 2004 | 132 | 2004 |
| Multiple roles of a conserved GAF domain tyrosine residue in cyanobacterial and plant phytochromes AJ Fischer, NC Rockwell, AY Jang, LA Ernst, AS Waggoner, Y Duan, ... Biochemistry 44 (46), 15203-15215, 2005 | 121 | 2005 |
