Research Topics
| Yong DuanSummaryAffiliation: University of Delaware Country: USA Publications
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Detail Information
Publications
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculationsYong Duan
Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
J Comput Chem 24:1999-2012. 2003..charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed...- The binding of thioflavin T and its neutral analog BTA-1 to protofibrils of the Alzheimer's disease Abeta(16-22) peptide probed by molecular dynamics simulationsChun Wu
Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
J Mol Biol 384:718-29. 2008.... - Loop conformation and dynamics of the Escherichia coli HPPK apo-enzyme and its binary complex with MgATPRong Yang
Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
Biophys J 89:95-106. 2005..The lessons learned here offer valuable structural insights into the workings of HPPK and should be useful for structure-based drug design... - Statistical characterization of salt bridges in proteinsJames N Sarakatsannis
Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
Proteins 60:732-9. 2005..In particular, it was shown that there is a strong correlation between secondary structure and salt bridge formation, and that salt bridges display preferential formation in an environment of about 30% solvent accessible surface area... - Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptideShibasish Chowdhury
Department of Chemistry and Biochemistry, Center of Biomedical Research Excellence, University of Delaware, Newark, DE 19716, USA
Biopolymers 68:63-75. 2003..Instead, the rate-limiting step for this peptide is breaking the non-native hydrophobic clusters in order to reach the transition state. The implication to the folding mechanisms of proteins is also discussed... - Convergence of replica exchange molecular dynamicsWei Zhang
Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
J Chem Phys 123:154105. 2005..Other technical issues, including choice of exchange frequency, were also examined... - Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolutionShibasish Chowdhury
Department of Chemistry and Biochemistry, Center of Biomedical Research Excellence in Structural and Functional Genomics, University of Delaware, Newark, DE 19716, USA
J Mol Biol 327:711-7. 2003..Analysis of the trajectory suggests that the rate-limiting step of folding of this mini-protein is the packing of the Trp side-chain... - Solvation effects on alanine dipeptide: A MP2/cc-pVTZ//MP2/6-31G** study of (Phi, Psi) energy maps and conformers in the gas phase, ether, and waterZhi-Xiang Wang
Department of Chemistry and Biochemistry, University of Delaware, 222 S. Chapel St, Newark, Delaware 19716, USA
J Comput Chem 25:1699-716. 2004..The energy surfaces may serve as the basis for developing of strategies enabling the inclusion of solvent polarization in the force field... - Grow to Fit Molecular Dynamics (G2FMD): an ab initio method for protein side-chain assignment and refinementWei Zhang
Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
Protein Eng Des Sel 19:55-65. 2006..However, the accuracy decreased when exposed side chains were involved. Further improvement and application of the method and the possible reasons that affect the accuracy on the exposed side chains are discussed... - Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent modelMathew C Lee
Department of Chemistry and Biochemistry and Center of Biomedical Research Excellence in Structural and Functional Genomics, University of Delaware, Newark 19716, USA
Proteins 55:620-34. 2004..The results of our study showed that our new scoring function represents a significant improvement over previously published physics-based scoring functions... - Formation of partially ordered oligomers of amyloidogenic hexapeptide (NFGAIL) in aqueous solution observed in molecular dynamics simulationsChun Wu
Department of Chemistry and Biochemistry and Center of Biomedical Research Excellence in Structural and Functional Genomics, University of Delaware, Newark, 19716, USA
Biophys J 87:3000-9. 2004.... - Elongation of ordered peptide aggregate of an amyloidogenic hexapeptide NFGAIL observed in molecular dynamics simulations with explicit solventChun Wu
Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
J Am Chem Soc 127:13530-7. 2005..Taken together, these results offered a glimpse at the molecular events leading to the formation of ordered and disordered low-weight oligomers... - Comparison between Generalized-Born and Poisson-Boltzmann methods in physics-based scoring functions for protein structure predictionMatthew C Lee
Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
J Mol Model 12:101-10. 2005..We also discussed the effect to the scoring function accuracy due to presence of large ligands and ions in some native structures of the decoy sets... - Large-scale conformational dynamics of the HIV-1 integrase core domain and its catalytic loop mutantsMatthew C Lee
Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
Biophys J 88:3133-46. 2005..The findings reported here provide a detailed view of the active site conformational dynamics and should be useful for structure-based inhibitor design for integrase... - Conformational changes in protein functionHaiguang Liu
Genome Center, University of California, Davis, CA, USA
Methods Mol Biol 443:258-75. 2008.... - Chromophore channeling in the G-protein coupled receptor rhodopsinTing Wang
Genome Center and Bioinformatics Program and Department of Applied Science, 431 East Health Science Drive, University of California, Davis, California 95616-8816, USA
J Am Chem Soc 129:6970-1. 2007 - Protein folding and unfolding by all-atom molecular dynamics simulationsHongxing Lei
Genome Center, University of California, Davis, CA, USA
Methods Mol Biol 443:277-95. 2008..The popular replica exchange method was chosen to represent sampling approaches. Our emphasis is placed on the analysis of the simulation trajectories, and some in-depth discussions are provided for commonly encountered problems... - Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulationsHongxing Lei
Genome Center and Department of Applied Science, University of California, Davis, CA 95616, USA
Proc Natl Acad Sci U S A 104:4925-30. 2007..A comprehensive picture of the kinetics and thermodynamics of HP35 folding emerges when the results from replica exchange and conventional molecular dynamics simulations are combined... - Statistical properties and kinetics of end-end contact formation of unfolded polypeptides: a systematic molecular dynamics studyGuanghui Ping
UC Davis Genome Center, University of California, Davis, California 95616, USA
J Chem Phys 126:045108. 2007..However, notable deviation from the ideal Gaussian chain model was observed at lower temperatures particularly for those polypeptides without glycines, due to the tendency to form local structures... - Dual binding modes of Congo red to amyloid protofibril surface observed in molecular dynamics simulationsChun Wu
UC Davis Genome Center and Department of Applied Science, University of California, Davis, California 95616, USA
J Am Chem Soc 129:1225-32. 2007..Two potential inhibition mechanisms of disrupting beta-sheet stacking were inferred from the primary mode, which could be exploited for the development of non-peptidic amyloid-specific inhibitors... - Phenol red interacts with the protofibril-like oligomers of an amyloidogenic hexapeptide NFGAIL through both hydrophobic and aromatic contactsChun Wu
Genome Center and Department of Applied Science, University of California, Davis, California 95616, USA
Biophys J 91:3664-72. 2006..Further free energy analysis suggested that a phenol red analog may potentially improve the binding affinity... - Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulationsHongxing Lei
UC Davis Genome Center and Department of Applied Science, University of California at Davis, One Shields Avenue, Davis, California 95616, USA
J Chem Phys 128:235105. 2008..Based on the lowest physical energy, the predicted structure was 2.0 A C(alpha) RMSD away from the experimentally determined structure... - The role of plastic beta-hairpin and weak hydrophobic core in the stability and unfolding of a full sequence design proteinHongxing Lei
Bioinformatics Program and Department of Applied Science, University of California, Davis, California 95616, USA
J Chem Phys 121:12104-11. 2004..The loss of global contacts from the separation further destabilized the hairpin structure and also led to the unwinding of the helix... - Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptidesZhi-Xiang Wang
UC Davis Genome Center, 431 East Health Sciences Drive, University of California, Davis, California 95616-8816, USA
J Comput Chem 27:781-90. 2006..rl demonstrated good balance among these three important regions. The optimized torsion parameters, together with those in ff02, allow us to carry out simulations on proteins and peptides with the consideration of polarization... - Molecular dynamics simulations and free energy analyses on the dimer formation of an amyloidogenic heptapeptide from human beta2-microglobulin: implication for the protofibril structureHongxing Lei
UC Davis Genome Center and Department of Applied Science, One Shields Avenue, Davis, CA 95616, USA
J Mol Biol 356:1049-63. 2006..A double-layer protofibril structure is also proposed in which two antiparallel beta-sheets face each other and are held together by hydrophobic staples and hydrogen bonds of the polar side-chains... - Incorporating intermolecular distance into protein-protein dockingHongxing Lei
UC Davis Genome Center and Bioinformatics Program, Department of Applied Science, University of California, One Shields Avenue, Davis, CA 95616, USA
Protein Eng Des Sel 17:837-45. 2004..The composite score had successful prediction for 13 of the 15 antibody-antigen targets... - The role of Phe in the formation of well-ordered oligomers of amyloidogenic hexapeptide (NFGAIL) observed in molecular dynamics simulations with explicit solventChun Wu
Genome Center and Department of Applied Science, University of California, Davis, California 95616, USA
Biophys J 88:2897-906. 2005..The disordered oligomers were mainly stabilized by nonspecific hydrophobic interactions, whereas the well-ordered oligomers were further stabilized by cross-strand hydrogen bonds and favorable side-chain stacking... - Effects of posttranslational modifications on the structure and dynamics of histone H3 N-terminal PeptideHaiguang Liu
UC Davis Genome Center and Department of Applied Science, University of California, Davis, California 95616, USA
Biophys J 94:4579-85. 2008..In light of the existing experimental evidence, we propose that the changes in the dynamics of the modified variants contribute to their different functional roles... - Two-way effects between hydrogen bond and intramolecular resonance effect: an ab initio study on complexes of formamide and its derivatives with waterTao Liu
College of Chemistry and Chemical Engineering, Graduate University of Chinese Academy of Sciences, Beijing 100049, P R China
J Phys Chem A 112:5436-47. 2008..The study supports Pauling's resonance model... - Binding modes of CCR5-targetting HIV entry inhibitors: partial and full antagonistsTing Wang
Genome Center and Bioinformatics Program and Department of Applied Science, 431 East Health Science Drive, University of California, Davis, CA 95616 8816, USA
J Mol Graph Model 26:1287-95. 2008..These results could help design HIV co-receptor activity-specific inhibitors... - Two-stage folding of HP-35 from ab initio simulationsHongxing Lei
Genome Center and Department of Applied Science, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
J Mol Biol 370:196-206. 2007..The folding intermediate further acted as a template that facilitated the folding and docking of helix I in the second stage. Detailed descriptions of the folding kinetics and the roles of key residues are presented... - Ab initio folding of albumin binding domain from all-atom molecular dynamics simulationHongxing Lei
Genome Center and Department of Applied Science, One Shields Avenue, Davis, California 95616, USA
J Phys Chem B 111:5458-63. 2007..The slightly shifted boundaries of the helical segments had direct impact on the global packing, suggesting room for improvement on the simulation force field and solvation model... - Improved sampling methods for molecular simulationHongxing Lei
UC Davis Genome Center and Department of Applied Science, University of California, Davis, CA 95616, USA
Curr Opin Struct Biol 17:187-91. 2007..Significant progress has been made in the past couple of years, with emerging methods targeting specific aspects of the potential energy surface and new variants of the replica exchange method... - Folding transition-state and denatured-state ensembles of FSD-1 from folding and unfolding simulationsHongxing Lei
UC Davis Genome Center and Department of Applied Science, University of California, Davis, California 95616, USA
J Phys Chem B 110:22001-8. 2006.... - Denatured-state ensemble and the early-stage folding of the G29A mutant of the B-domain of protein AShibasish Chowdhury
University of California-Davis Genome Center and Bioinformatics Program, Department of Applied Science, University of California, One Shields Avenue, Davis, California 95616, USA
J Phys Chem B 109:9073-81. 2005..Apparently, destabilization of nonnative states dramatically enhanced the folding rates... - New-generation amber united-atom force fieldLijiang Yang
Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
J Phys Chem B 110:13166-76. 2006..The new united-atom force field is at least a factor of 200 more efficient than the Duan et al. all-atom force field for ab initio folding of the tested peptide...