Yong Duan

发表

Improved sampling methods for molecular simulation.

Hongxing Lei, Yong Duan, Y. Duan, 2007, Current opinion in structural biology.

Incorporating intermolecular distance into protein-protein docking.

Hongxing Lei, Yong Duan, 2004, Protein engineering, design & selection : PEDS.

Functional Networking of Human Divergently Paired Genes (DPGs)

Hongxing Lei, Yong Duan, Jun Yu, 2013, PloS one.

Grow to Fit Molecular Dynamics (G2FMD): an ab initio method for protein side-chain assignment and refinement.

Wei Zhang, Yong Duan, 2006, Protein engineering, design & selection : PEDS.

Large-scale conformational dynamics of the HIV-1 integrase core domain and its catalytic loop mutants.

Yong Duan, Y. Duan, J. Briggs, 2005, Biophysical journal.

Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations.

Chun Wu, Hongxing Lei, Yaoqi Zhou, 2008, The Journal of chemical physics.

Convergence of replica exchange molecular dynamics.

Chun Wu, Wei Zhang, Yong Duan, 2005, The Journal of chemical physics.

Statistical characterization of salt bridges in proteins

Yong Duan, Y. Duan, James N Sarakatsannis, 2005, Proteins.

Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution.

Shibasish Chowdhury, Yong Duan, Y. Duan, 2003, Journal of molecular biology.

Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide.

Chun Wu, Shibasish Chowdhury, Wei Zhang, 2003, Biopolymers.

Retinal release from opsin in molecular dynamics simulations

Ting Wang, Yong Duan, Y. Duan, 2011, Journal of molecular recognition : JMR.

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

Jie Li, Ray Luo, Piotr Cieplak, 2011, The journal of physical chemistry. B.

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

Ray Luo, Piotr Cieplak, Qin Cai, 2012, The journal of physical chemistry. B.

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

Yong Duan, Y. Duan, Zhi‐Xiang Wang, 2004, J. Comput. Chem..

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

Jie Li, Ray Luo, Piotr Cieplak, 2012, The journal of physical chemistry. B.

Insights into Ligand Binding to PreQ1 Riboswitch Aptamer from Molecular Dynamics Simulations

Yunjie Zhao, Yi Xiao, Yong Duan, 2014, PloS one.

Multiple roles of a conserved GAF domain tyrosine residue in cyanobacterial and plant phytochromes.

Hongxing Lei, Yong Duan, Y. Duan, 2005, Biochemistry.

Binding modes of CCR5-targetting HIV entry inhibitors: partial and full antagonists.

Ting Wang, Yong Duan, 2008, Journal of molecular graphics & modelling.

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

Yong Duan, Y. Duan, Mathew C. Lee, 2004, Proteins.

Comparison between Generalized-Born and Poisson–Boltzmann methods in physics-based scoring functions for protein structure prediction

Yong Duan, Y. Duan, Matthew C Lee, 2005, Journal of molecular modeling.

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

Jie Li, Ray Luo, Piotr Cieplak, 2011, The journal of physical chemistry. B.

Chromophore channeling in the G-protein coupled receptor rhodopsin.

Yong Duan, Y. Duan, Ting Wang, 2007, Journal of the American Chemical Society.

Polarization effects in molecular mechanical force fields

Piotr Cieplak, François-Yves Dupradeau, Yong Duan, 2009, Journal of physics. Condensed matter : an Institute of Physics journal.

Gradient SHAKE: An improved method for constrained energy minimization in macromolecular simulations

Peter A. Kollman, John M. Rosenberg, Yong Duan, 1995 .

Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48 G 7

Peter A. Kollman, Lu Wang, Irina Massova, 1999 .

Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation.

Hongxing Lei, Yong Duan, Y. Duan, 2007, The journal of physical chemistry. B.