Publication List of Yingkai Zhang

126. 1. Chao Han, Dongdong Zhang,Song Xia and Yingkai Zhang, J. Chem. Theory Comput., 20, 5250 - 5258 (2024).

Accurate Prediction of NMR Chemical Shifts: Integrating DFT Calculations with Three-Dimensional Graph Neural Networks

125. Nathan Soper, Isabelle Yardumian, Eric Chen, Chao Yang, Samantha Ciervo, Aaron Oom, Ludovic Desvignes, Mark Mulligan, Yingkai Zhang, Tania Lupoli ACS Chem. Biol., 19,1593 - 1603 (2024).

A repurposed drug interferes with nucleic acid to inhibit the dual activities of coronavirus Nsp13

124. Jianping Li, Ampon Sae Her, Alida Besch, Belen Ramirez-Cordero, Maureen Crames, James R Banigan, Casey Mueller, William M Marsiglia, Yingkai Zhang, Nathaniel J Traaseth Nature Comm., 15, 4537 (2024).

Dynamics underlie the drug recognition mechanism by the efflux transporter EmrE

123. Song Xia, Eric Chen and Yingkai Zhang, J. Chem. Theory Comput., 19, 7478 - 7495 (2023).

Integrated Molecular Modeling and Machine Learning for Drug Design

122. Angel D′Oliviera, Xuhang Dai, Saba Mottaghinia, Evan P. Geissler, Lucie Etienne, Yingkai Zhang, and Jeffrey S. Mugridge elife, 12, RP91168 (2023).

Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease

121. Zhiyuan Zhao, Jintong Du, Yu Du, Yuan Gao, Mingxuan Yu, Yingkai Zhang, Hao Fang, and Xuben Hou, J. Chem. Inf. Model., 63, 5896 - 5902 (2023).

Deciphering the Allosteric Activation Mechanism of SIRT6 Using Molecular Dynamics Simulations

120. Alida Besch, William M. Marsiglia, Moosa Mohammadi, Yingkai Zhang, and Nathaniel J. Traaseth Proc. Natl. Acad. Sci., 120, e2213090120 (2023).

Gatekeeper Mutations Activate FGF Receptor Tyrosine Kinases by Destabilizing the Autoinhibited State

119. Song Xia, Dongdong Zhang and Yingkai Zhang, J. Chem. Theory Comput., 19, 659 - 668 (2023).

Multitask Deep Ensemble Prediction of Molecular Energetics in Solution: From Quantum Mechanics to Experimental Properties

118. Xiao-Kang Guo and Yingkai Zhang, J. Chem. Inf. Model., 62, 6057 - 6068 (2022).

CovBinderInPDB: a Structure-based Covalent Binder Database

117. Chao Yang, Eric Anthony Chen and Yingkai Zhang, Molecules, 27,4568 (2022).

Protein-Ligand Docking in the Machine Learning Era

116. Chao Yang and Yingkai Zhang, J. Chem. Inf. Model., 62,2696-2712 (2022).

Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein-Ligand Scoring Functions

115. Dongdong Zhang, Song Xia and Yingkai Zhang, J. Chem. Inf. Model., 62, 1840-1848 (2022).

Accurate Prediction of Aqueous Solvation Free Energies using 3D Atomic Feature-based Graph Neural Network with Transfer Learning

114. Jieyu Lu and Yingkai Zhang, J. Chem. Inf. Model., 62, 1376-1387 (2022).

Unified Deep Learning Model for Multi-task Reaction Predictions with Explanation

113. Ashley E. Modell, Frank Marrone III, Nihar R. Panigrahi, Yingkai Zhang and Paramjit S. Arora, J. Am. Chem. Soc., 144, 1198-1204 (2022).

Peptide Tethering: Pocket-Directed Fragment Screening for Peptidomimetic Inhibitor Discovery

112. Christian Fischer, Nynke Veprek, Zisis Peitsinis, Peter Rühmann, Chao Yang, Jessica Spradlin, Dustin Dovala, Daniel Nomura, Yingkai Zhang, and Dirk Trauner, Synlett,33, 458 - 463 (2022).

De novo Design of SARS-CoV-2 Main Protease Inhibitor

111. Chao Yang and Yingkai Zhang, J. Chem. Inf. Model., 61, 4630 - 4644, (2021).

Lin_F9: a Linear Empirical Scoring Function for Protein-Ligand Docking

110. Justin Torner, Yuwei Yang, David Rooklin, Yingkai Zhang, Paramjit Arora, ACS Chem. Biol., 16, 1179 - 1183 (2021).

Identification of secondary binding sites on protein surfaces for rational elaboration of synthetic protein mimics

109. Kai Wen Teng, Steven Tsai, Takamitsu Hattori, Carmine Fedele, Akiko Koide, Chao Yang, Xuben Hou, Yingkai Zhang , Benjamin Neel, John O'Bryan, and Shohei Koide, Nature Commun., 12, 2656 (2021).

Selective and Noncovalent Targeting of RAS Mutants for Inhibition and Degradation

108. Yong Xia, Yan Liu, Chao Yang, Diane Simeone, Tung-Tien Sun, David Degraff, Moon-Shong Tang, Yingkai Zhang ,and Xue-Ru Wu, Nature Commun., 12, 2047 (2021).

Dominant role of CDKN2B/p15INK4B of 9p21.3 tumor suppressor hub in inhibition of cell-cycle and glycolysis

107. Jianing Lu, Song Xia, Jieyu Lu and Yingkai Zhang , J. Chem. Inf. Model., 61, 1095 - 1104 (2021)

Dataset Construction to Explore Chemical Space with 3D Geometry and Deep Learning

106. J. Zhao, A. Blayney, X. Liu, iL. Gandy, W. Jin, L. Yan, J.-H. Ha, A. J. Canning, M. Connelly, C. Yang, X. Liu, Y. Xiao, M. Cosgrove, S. Solmazh, Y. Zhang , D. Ban, J. Chen, S. N. Loh and C. Wang, Nature Commun., 12, 986 (2021).

EGCG Binds Intrinsically Disordered N-Terminal Domain of p53 and Disrupts p53-MDM2 Interaction

105. J. Katigbak, H. Li, D. Rooklin, and Y. Zhang , J. Chem. Inf. Model., 60,1494-1508(2020)

AlphaSpace 2.0: Representing Concave Biomolecular Surfaces using Beta-Clusters

104. J. Sadek, M. G. Wuo, D. Rooklin, A. Haunstein, S. H. Hong, A. Gautam, H. Wu, Y. Zhang , E. Cesarman, and P. S. Arora, Nature Commun., 11, 1786 (2020).

Modulation of Virus-Induced NF-kB Signaling by NEMO Coiled Coil Mimics

103. L. Chen, W. M. Marsiglia, H. Chen, J. Katigbak, H. Erdjument-Bromage, D. J. Kemble, L. Fu, J. Ma, G. Sun,Y. Zhang , G. Liang, T. A. Neubert, X. Li, N. J. Traaseth, and M. Mohammadi, Nature Chem. Biol., 16 , 267-277 (2020).

Molecular Basis for Receptor Tyrosine Kinase A-Loop Tyrosine Transphosphorylation

102. J. Du, W. Li, B. Liu, Y. Zhang , J. Yu, X. Hou and H. Fang, Biol. Med. Chem., 28, 115607 (2020).

An in silico mechanistic insight into HDAC8 activation facilitates the discovery of new small-molecule activators

101. J. Zhao, X. Liu, W. Xia, Y. Zhang , and C. Wang, Front. Mol. Neuroscii., 13, 137 (2020).

Targeting Amyloidogenic Processing of APP in Alzheimer’s Disease

100. X. Liu, J. Zhao, Y. Zhang ,I. Ubarretxena-Belandia, S. T. Forth, R. L. Lieberman, and C. Wang, Front. Mol. Neuroscii., 13, 65 (2020).

Substrate-enzyme interaction in intramembrane proteolysis: γ-secretase as the prototype

99. X. Hou, J.-P. Sun, L. Ge, X. Liang, K. Li, Y. Zhang , and H. Fang, Eur. J. Med. Chem., 190, 112131 (2020).

Inhibition of Striatal-enriched Protein Tyrosine Phosphatase by Targeting Computationally Revealed Cryptic Pockets

98. J. Zhao, Y. Xiao, X. Liu, S. Kim, X. Wu, M. Barros, R. Zhuang, X. Hou,Y. Zhang , N. K. Robakis, Y.-M. Li, J. S. Dordick, I. Ubarretxena-Belandia, and C. Wang, Chem. Commun., 56, 2578-2581 (2020).

Substrate interaction inhibits γ-secretase production of amyloid-β peptides

97. Y. Yang, J. Lu, C. Yang, and Y. Zhang , J. Comput. Aided Mol. Des., 33, 1095 - 1105 (2019).

Exploring Fragment-based Target Specific Ranking Protocol with Machine Learning on Cathepsin S

96. J. Lu, X. Hou, C. Wang, and Y. Zhang , J. Chem. Inf. Model., 59, 4540 - 4549 (2019)

Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions

95. J. Lu, C. Wang, and Y. Zhang , J. Chem. Theory Comput., 15, 4113 - 4121 (2019)

Predicting Molecular Energy using Force-Field Optimized Geometries and Atomic Vector Representations Learned from Improved Deep Tensor Neural Network

94. W. Marsiglia, J. Katigbak, S. Zheng, M. Mohammadi, Y. Zhang and N. Traaseth , Structure, 27, 1308 - 1315 (2019)

A Conserved Allosteric Pathway in Tyrosine Kinase Regulation

93. K. Li, X. Hou, R. Li, W. Bi, F. Yang, X. Chen, P. Xiao, T. Liu, T. Lu, Y. Zhou, Z. Tian, Y. Shen, Y. Zhang , J. Wang, H. Fang, J. Sun, X. Yu, J. Biol. Chem. , 294 , 8653 - 8663 (2019).

Identification and structure-function analyses of an allosteric inhibitor of the tyrosine phosphatase PTPN22.

92. C. Tse, J. Xu, L. Xu, F. K. Sheong, S. Wang, H. Y. Chow, X. Gao, X. Li, P. Cheung, D. Wang, Y. Zhang, and X. Huang, Nature Catalysis , 2 , 228 - 235 (2019).

Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-independent Mechanism Assisted by Transcript Phosphate.

91. J. Lei, G. Sheng, P. P.-H. Cheung, S. Wang, Y. Li, X. Gao, Y. Zhang, Y. Wang and X. Huang, Proc. Natl. Acad. Sci. , 116 , 845-853 (2019).

Two Symmetric Arginine Residues Play Distinct Roles in Thermus thermophilus Argonaute DNA Guide Strand-mediated DNA Target Cleavage.

90. X. Hou, D. Rooklin, D. Yang, X. Liang, K. Li, J. Lu, C. Wang, P. Xiao, Y. Zhang, J.-P. Sun, and H. Fang, J. Chem. Inf. Model. , 58 , 2331-2342 (2018).

Computational strategy for bound state structure prediction in structure-based virtual screening: a case study of protein tyrosine phosphatase receptor type O inhibitors.

89. H. Mu, Y. Zhang, N. Geacintov, and S. Broyde, Chem. Res. Toxicol. , 31 , 1260-1268 (2018).

Lesion sensing during initial binding by yeast XPC/Rad4: toward predicting resistance to nucleotide excision repair.

88. L. Qiu, J. Song, Y. Zhang and J. Zhang, Mol. Phys. , 116 , 2613-2621 (2018).

Functional Loop Dynamics of the S-Component of ECF Transporter FolT.

87. Y. Cai, I. Fu, N. Geacintov, Y. Zhang and S. Broyde, DNA Repair , 65 , 73-78 (2018).

Synergistic effects of H3 and H4 nucleosome tails on structure and dynamics of a lesion-containing DNA: Binding of a displaced lesion partner base to the H3 tail for GG-NER recognition.

86. D. W. Rooklin, A. E. Modell, H. Li, V. Berdan, P. S. Arora, and Y. Zhang, J. Am. Chem. Soc. , 139 , 15560-15563 (2017).

Targeting Unoccupied Surfaces on Protein-Protein Interfaces.

85. C. Wang and Y. Zhang, J. Comput. Chem. , 38 , 169-177 (2017).

Improving Scoring-Docking-Screening Powers of Protein-Ligand Scoring Functions using Random Forest

84. H. Mu, N. E. Geacintov,J. H. Min, Y. Zhang, and S. Broyde, Chem Res Toxicol. , 30 , 1344 - 1354 (2017).

The nucleotide excision repair lesion-recognition protein Rad4 captures a pre-flipped partner base in a benzo[a]pyrene-derived DNA lesion: how structure impacts the binding pathway.

83. C. Chen, X. Hou, G. Wang, W. Pan, X. Yang, Y. Zhang, and H. Fang, Eur. J. Med. Chem. , 133,11-23 (2017).

Design, synthesis and biological evaluation of quinoline derivatives as HDAC class I inhibitors

82. I. Fu, Y. Cai, Y. Zhang, N. E. Geacintov, and S. Broyde, Biochemistry , 56 ,1963-1973 (2017).

Nucleosome histone tail conformation and dynamics: impacts of lysine acetylation and a nearby minor groove benzo[a]pyrene-derived lesion

81. X. Hou, D. Rooklin, H. Fang and Y. Zhang, Sci. Rep. , 6,38186 (2016).

Resveratrol Serves as a Protein-Substrate Interaction Stabilizer in Human SIRT1 Activation

80. Y. Zhou, S. Wang, Y. Li and Y. Zhang, Methods in Enzymology , 577,105-118 (2016).

Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions

79. H. Hu, J. B. Diccianni, J. Katigbak, C. Hu, Y. Zhang, and T. Diao, J. Am. Chem. Soc. , 138, 4779-4786 (2016).

Bimetallic C-C Bond-Forming Reductive Elimination from Nickel

78. Y. Zhou, D. Xie and Y. Zhang, J. Phys. Chem. Lett. , 7, 1138-1142 (2016).

Amide Rotation Hindrance Predicts Proteolytic Resistance of Cystine-Knot Peptides

77. I. Fu, Y. Cai, Y. Zhang, N. E. Geacintov, and S. Broyde, Biochemistry , 55 , 239 - 242 (2016).

Entrapment of a Histone Tail by a DNA Lesion in a Nucleosome Suggests the Lesion Impacts Epigenetic Marking: A Molecular Dynamics Study

76. D. W. Rooklin, C. Wang, J. Katigbak, P. S. Arora, and Y. Zhang, J. Chem. Inf. Model. , 55 , 1585 - 1599 (2015).

AlphaSpace: Fragment-Centric Topographical Mapping to Target Protein-Protein Interaction Interfaces

75. W. Gong, R. Wu, and Y. Zhang, J. Comput. Chem. , 36 , 2228 - 2235 (2015).

Thiol versus Hydroxamate as Zinc Binding Group in HDAC Inhibition: An ab initio QM/MM Molecular Dynamics Study

74. H. Mu, N. E. Geacintov, Y. Zhang, and S. Broyde, Biochemistry , 54 , 5263 - 5267 (2015).

Recognition of Damaged DNA for Nucleotide Excision Repair: A Correlated Motion Mechanism with a Mismatched cis-syn Thymine Dimer Lesion

73. J. Lei, Y. Zhou, D. Xie and Y. Zhang, J. Am. Chem. Soc. , 137, 70-73 (2015).

Mechanistic Insights into a Classic Wonder Drug - Aspirin

72. N. Zhou, Q. Wu, and Y. Zhang, ``Force field development with density-based energy decomposition analysis ,''

in Many-body effects and electrostatics in multi-scale computation of Biomolecules (Qiang Cui, Markus Meuwly and Pengyu Ren, eds.) , 2015.

71. J. Zhou, M. Li, N. Chen, S. Wang, H. B. Luo, Y. Zhang, and R. Wu, ACS Chem. Biol. , 10 , 687-692 (2015).

Computational Design of a Time-Dependent Histone Deacetylase 2 Selective Inhibitor

70. X. Xiao, N. Kallenbach and Y. Zhang, J. Chem. Theory Comput., 10, 4152-4159 (2014).

Peptide Conformation Analysis using an Integrated Bayesian Approach

69. L. Lior-Hoffmann, S. Ding, N. E. Geacintov, Y. Zhang and S. Broyde, Biochemistry, 53, 5683-5691 (2014).

Structural and Dynamic Characterization of Polymerase k's Minor Groove Lesion Processing Reveals How Adduct Topology Impacts Fidelity

68. N. Zhou, Z. Lu, Q. Wu and Y. Zhang, J. Chem. Phys., 140, 214117 (2014).

Improved parameterization of interatomic potentials for rare gas dimers with density-based energy decomposition analysis

67. G. S. Sirin, Y. Zhang , J. Phys. Chem. A, 118,9132-9139 (2014)

How is Acetylcholinesterase Phosphonylated by Soman? An ab initio QM/MM Molecular Dynamics Study

66. Y. Cai, H. Zheng, S. Ding, K. Kropachev, A. G. Schwaid, Y. Tang, H. Mu, S. Wang, N. Geacintov, Y. Zhang and S. Broyde,

Chem. Res. Toxicol, 26, 1115-1125 (2013).

Free Energy Profiles of Base Flipping in Intercalative Polycyclic Aromatic Hydrocarbon-Damaged DNA Duplexes: Energetic and Structural Relationships to Nucleotide Excision Repair Susceptibility

65. J. Yang, L. Lior-Hoffmann, S. Wang, Y. Zhang , and S. Broyde, Biochemistry, 52, 2828-2838 (2013)

DNA cytosine methylation: Structural and thermodynamic characterization of the epigenetic marking mechanism

64. Y. Shi, Y. Zhou, S. Wang, Y. Zhang , J. Phys. Chem. Lett., 4 , 491-495 (2013)

Sirtuin Deacetylation Mechanism and Catalytic Role of the Dynamic Cofactor Binding Loop

63. G. S. Sirin, Y. Zhou,L. Lior-Hoffmann, S. Wang, Y. Zhang , J. Phys. Chem. B, 116, 12199-12207 (2012)

Aging Mechanism of Soman Inhibited Acetylcholinesterase

62. D. W. Rooklin, M. Lu, Y. Zhang , J. Am. Chem. Soc., 134, 15595-15603 (2012)

Revelation of a Catalytic Calcium-Binding Site Elucidates Unusual Metal Dependence of a Human Apyrase

61. L. Lior-Hoffmann, L. Wang, S. Wang, N. Geacintov, S. Broyde and Y. Zhang , Nucleic Acids Res., 40, 9193-9205 (2012)

Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase k elucidates error-free bypass of a bulky DNA lesion

60. Y. Zhou, S. M. Moin, S. Urban, Y. Zhang , Structure, 20, 1255-1263 (2012)

An Internal Water Retention Site in the Rhomboid Intramembrane Protease GlpG Ensures Catalytic Efficiency

59. R. Wu, Z. Cao, Y. Zhang Progress in Chemistry, 24,1175-1184 (2012)

Computational Simulations of Zinc Enzyme: Challenges and Recent Advances

58. R. Wu, W. Gong, T. Liu, Y. Zhang and Z. Cao, J. Phys. Chem. B, 116, 1984-1991 (2012)

QM/MM Molecular Dynamics Study of Purine-Specific Nucleoside Hydrolase

57. Z. Lu, N. Zhou, Q. Wu, Y. Zhang, J. Chem. Theory Comput.,7, 4038-4049 (2011).

Directional Dependence of Hydrogen Bonds: a Density-based Energy Decomposition Analysis and Its Implications on Force Field Development

56. Z. Ke, G. Smith, Y. Zhang and H. Guo, J. Am. Chem. Soc., 133, 11103-11105 (2011)

Molecular Mechanism for Eliminylation, a Newly Discovered Post-Translational Modification

55. R. Wu, Z. Lu, Z. Cao and Y. Zhang, J. Am. Chem. Soc., 133, 6110-6113 (2011).

Zinc Chelation with Hydroxamate in Histone Deacetylases Modulated by Water Access to the Linker Binding Channel

54. Z. Ke, H. Guo, D. Xie, S. Wang and Y. Zhang, J. Phys. Chem. B, 115, 3725-3733, (2011).

Ab Initio QM/MM Free-Energy Studies of Arginine Deiminase Catalysis: The Protonation State of the Cys Nucleophile.

53. R. Wu, Z. Lu, Z. Cao and Y. Zhang, J. Chem. Theory Comput., 7, 433-443 (2011).

A Transferable Non-bonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins

52. Y. Zhou and Y. Zhang, ChemComm, 47, 1577-1579 (2011).

Serine Protease Acylation Proceeds with a Subtle Re-orientation of the Histidine Ring at the Tetrahedral Intermediate

51. H. Zheng, Y. Cai, S. Ding, Y. Tang, K. Kropachev, Y. Zhou, L. Wang, S. Wang, N. Geacintov, Y. Zhang and S. Broyde,

Chem. Res. Toxicol, 23, 1868-1870 (2010). Base Flipping Free Energy Profiles for Damaged and Undamaged DNA.

50. H. B. Xie, Y. Zhou, Y. Zhang and J. K. Johnson, J. Phys. Chem. A, 114, 11844-11852 (2010).

Reaction Mechanism of Monoethanolamine with CO2 in Aqueous Solution from Molecular Modeling

49. R. Wu, S. Wang, N. Zhou, Z. Cao and Y. Zhang, J. Am. Chem. Soc. , 132, 9471-9479 (2010).

A Proton-Shuttle Reaction Mechanism for Histone Deacetylase 8 and the Catalytic Role of Metal Ions

48. Y. Zhou, S. Wang and Y. Zhang, J. Phys. Chem. B, 114, 8817-8825 (2010).

Catalytic Reaction Mechanism of Acetylcholinesterase Determined by Born-Oppenheimer ab initio QM/MM Molecular Dynamics Simulations

47. R. Wu, P. Hu, S. Wang, Z. Cao and Y. Zhang, J. Chem. Theory Comput., 6, 337-343 (2010).

Flexibility of Catalytic Zinc Coordination in Thermolysin and HDAC8: A Born-Oppenheimer

ab initio QM/MM Molecular Dynamics Study

46. Z. Ke, S. Wang, D. Xie and Y. Zhang, J. Phys. Chem. B, 113, 16705-16710 (2009).

Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of the Hydrolysis Reaction Catalyzed

by Protein Arginine Deiminase 4

45. J. Liu, Y. Zhang and C. G. Zhan, J. Phys. Chem. B, 113, 16226-16236 (2009) .

Reaction Pathway and Free Energy Barrier for Reactivation of Dimethylphosphoryl-inhibited Human Acetylcholinesterase

44. H. Zheng and Y. Zhang, J. Chem. Phys., 131, 214105 (2009).

Introducing Sampling Entropy in Repository Based Adaptive Umbrella Sampling

43. Q. Wu, P. W. Ayers and Y. Zhang, J. Chem. Phys., 131, 164112 (2009).

Density-based energy decomposition analysis for intermolecular interactions with variationally determined intermediate state energies

42. K. Fahie, P. Hu, S. Swatkoski, R. Cotter, Y. Zhang, and C. Wolberger. FEBS J., 276, 7159-7176 (2009).

Side chain specificity of ADP-ribosylation by a sirtuin

41. Z. Lu, J. Lai, Y. Zhang, J. Am. Chem. Soc. , 131, 14928-14931 (2009).

Importance of Charge Independent Effects in Readout the Trimethyllysine Mark by HP1 Chromodomain.

40. H. Zheng, S. Wang and Y. Zhang, J. Comput. Chem., 30, 2706-2711 (2009).

Increasing the Time Step with Mass Scaling in Born-Oppenheimer ab initio QM/MM Molecular Dynamics Simulations

39. Z. Ke, Y. Zhou, P. Hu, S. Wang, D. Xie and Y. Zhang, J. Phys. Chem. B, 113, 12750-12758, (2009). ( Cover)

Active Site Cysteine Is Protonated in the PAD4 Michaelis Complex: Evidence from Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations

38. L. Wang, S. Broyde and Y. Zhang, J. Mol. Biol., 389, 787-796 (2009).

Polymerase-tailored Variations in the Water-Mediated and Substrate-Assisted Mechanism for Nucleotidyl Transfer: Insights from a Study of T7 DNA Polymerase

37. Y. Zhang, Ab Initio Quantum Mechanical/Molecular Mechanical Studies of Histone Modifying Enzymes. in Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications., 341-350, Darrin M. York and Tai-Sung Lee eds., Springer Verlag, New York, 2009.

36. P. Hu, S. Wang and Y. Zhang, J. Am. Chem. Soc. , 130, 16721-16728 (2008).

A Highly Dissociative and Concerted Mechanism for the Nicotinamide Cleavage Reaction in Sir2Tm Enzyme Suggested by ab initio QM/MM Molecular Dynamics Simulations

35. Z. Lu and Y. Zhang, J. Chem. Theory Comp., 4, 1237-1248 (2008).

Interfacing ab initio Quantum Mechanical Method with Classical Drude Osillator Polarizable Model for Molecular Dynamics Simulation of Chemical Reactions

34. H. Zheng and Y. Zhang, J. Chem. Phys. ,128, 204106 (2008).

Determination of Free Energy Profiles by Repository Based Adaptive Umbrella Sampling: Bridging Nonequilibrium and Quasiequilibrium Simulations

33. P. Hu, S. Wang and Y. Zhang, J. Am. Chem. Soc. , 130, 3806-3813 (2008).

How do SET-domain Protein Lysine Methyltransferases Achieve the Methylation State Specificity ? Revisited by ab initio QM/MM Molecular Dynamics Simulations.

32. Z. Liu, A. W. Young, P. Hu, A. J. Rice, C. Zhou, Y. Zhang and N. R. Kallenbach, ChemBioChem , 8, 2063-2065 (2007).

Tuning Selectivity of Antimicrobial Peptides by Multivalent Design.

31. C. Xiao and Y. Zhang, J. Chem. Phys., 127, 124102 (2007).
Design-Atom Approach for the Quantum Mechanical/Molecular Mechanical Covalent Boundary: A Design-Carbon Atom with Five Valence Electrons.

30. C. Xiao and Y. Zhang, J. Phys. Chem. B , 111, 6229-6235 (2007).
Catalytic Mechanism and Metal Specificity of Bacterial Peptide Deformylase: a Density Functional Theory QM/MM Study.

29. L. Wang, X. Yu, P. Hu, S. Broyde and Y. Zhang, J. Am. Chem. Soc. , 129, 4731-4737 (2007).
A Water-mediated and Substrate-assisted Catalytic Mechanism for Sulfolobus solfataricus DNA Polymerase IV

28. S. Wang, P. Hu and Y. Zhang, J. Phys. Chem. B , 111, 3758-3764 (2007).
Ab initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation of Enzyme Catalysis: The Case of Histone Lysine Methyltransferase SET7/9

27. C. Corminboeuf, P. Hu, M. E. Tuckerman and Y. Zhang, J. Am. Chem. Soc. , 128, 4530-4531 (2006).
Unexpected Deacetylation Mechanism Suggested by a Density Functional Theory QM/MM Study of Histone-Deacetylase-Like Protein

26. P. Hu and Y. Zhang, J. Am. Chem. Soc. , 128, 1272-1278 (2006).
Catalytic Mechanism and Product Specificity of the Histone Lysine Methyltransferase SET7/9. An ab initio QM/MM-FE
Study with Multiple Initial Structures.

25. Y. Cheng, Y. Zhang and J. A. McCammon, Protein Sci. , 15, 672-683 (2006).
How does Activation Loop Phosphorylation Modulate Catalytic Activity in the cAMP-dependent Protein Kinase:
A Theoretical Study.

24. V. V. Karambelkar, C. Xiao, Y. Zhang, A. Sarjeant and D. P. Goldberg, Inorg. Chem. , 45, 1409--1411 (2006).
Geometric Preferences in Iron(II) and Zinc(II) Model Complexes of Peptide Deformylase.

23. Y. Zhang, Theor. Chem. Acc. , Special Issue of ``New Perspectives in Theoretical Chemistry'' , 116, 43-50 (2006).
Pseudobond ab initio QM/MM approach and its Applications to Enzyme Reactions.

22. C. F. Wong, J. Kua, Y. Zhang, T. P. Straatsma and J. A. McCammon, Proteins, 61, 850-858 (2005).
Molecular Docking of Balanol to Dynamics Snapshots of Protein Kinase A.

21. X. H. Chen, Y. Zhang, J. Z.H. Zhang, J. Chem. Phys., 122, 184105 (2005).
An efficient approach for ab initio energy calculation of biopolymers.

20. Y. Zhang, J. Chem. Phys., 122, 024114 (2005).
Improved Pseudobonds for Combined ab initio Quantum Mechanical/Molecular Mechanical (QM/MM) Methods.

19. Y. Cheng, Y. Zhang, and J. A. McCammon, J. Am. Chem. Soc., .127, 1553 -1562 (2005).
How Does the cAMP-Dependent Protein Kinase Catalyze the Phosphorylation Reaction: an ab initio QM/MM Study

18. A. M. Gao, D.W. Zhang, J. Z.H. Zhang and Y. Zhang , Chem. Phys. Lett., 394, 293-297 (2004).
An efficient linear scaling method for ab initio calculation of electron density of proteins.

17. J. Kua, Y. Zhang, A. C. Eslami, J. R. Butler, and J. A. McCammon, Protein Sci., 12, 2675-2684 (2003)
Studying the Roles of W86, E202, Y337 in Binding of Acetylcholine to Acetylcholinesterase using a Combined Molecular Dynamics and Multiple Docking Approach

16. G. A. Cisneros, H. Liu, Y. Zhang, and W. Yang, J. Am. Chem. Soc., 125, 10384-10393 (2003).
Ab Initio QM/MM Study Shows There Is No General Acid in the Reaction Catalyzed by 4-Oxalocrotonate Tautomerase

15. Y. Zhang, J. Kua and J. A. McCammon, J. Phys. Chem. B, 107, 4459-4463 (2003).
Influence of Structural Fluctuation on Enzyme Reaction Energy Barriers in Combined Quantum Mechanical/Molecular Mechanical Studies.

14. Y. Zhang and J. A. McCammon, J. Chem. Phys., 118, 1821-1827 (2003).
Studying the Affinity and Kinetics of Molecular Association with Molecular Dynamics Simulation.

13. Y. Zhang, J. Kua and J. A. McCammon, J. Am. Chem. Soc., 124, 10572-10577 (2002).
Role of the Catalytic Triad and Oxyanion Hole in Acetylcholinesterase Catalysis: An ab initio QM/MM Study.

12. J. Kua, Y. Zhang and J. A. McCammon, J. Am. Chem. Soc., 124, 8260-8267 (2002).
Studying Enzyme Binding Specificity in Acetylcholinesterase using a Combined Molecular Dynamics and Multiple Docking Approach.

11. Y. Zhang, H. Liu, and W. Yang, ``Ab initio qm/mm and free energy calculationsof enzyme reactions,''
in Computational Methods for Macromolecules -Challenges and Applications (T.~Schlick and H.~H. Gan, eds.), 332-354, Springer-Verlag, 2002.

10. Y. Zhang, H. Liu and W. Yang , J. Chem. Phys, 112, 3483-3492 (2000).

Free energy calculations on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential

9. H. Liu, Y. Zhang and W. Yang , J. Am. Chem. Soc. , 122, 6560-6570 (2000).
How is the active site of enolase organized to catalyze two different reaction steps?

8. W. Yang, Y. Zhang and P. W. Ayers, Phys. Rev. Lett., 84, 5172-5175 (2000).
Degenerate Ground States and a Fractional Number of Electrons in Density and Reduced Density Matrix Functional Theory,

7. Y. Zhang and W. Yang, Theore. Chem. Acc., 103, 346-348 (2000).
Perspective on ``Density-Functional Theory for Fractional Particle Number:Derivative Discontinuities of the Energy'' by J.P. Perdew, R.G. Parr,M. Levy and J.L. Balduz,Jr.

6. C. Enkvist, Y. Zhang and W. Yang, Int. J. Quan. Chem., 79, 325-329 (2000).
Density Functional Study of a Weakly Hydrogen Bonded Benzene-Ammonia Complex: the Importance of the Exchange Functional .

5. Y. Zhang, T. S. Lee and W. Yang, J. Chem. Phys., 110, 46-54 (1999).
A Pseudobond Approach to Combining Quantum Mechanical and Molecular Mechanical Methods.

4. Y. Zhang and W. Yang, J. Chem. Phys.,109, 2604-2608 (1998).
A Challenge for Density Functionals: Self-interaction Error Increases for Systems with a Noninteger Number of Electrons.

3. Y. Zhang and W. Yang, Phys. Rev. Lett., 80, 890 (1998).
Comment on "Generalized Gradient Approximation Made Simple" .

2. Y. Zhang, W. Pan and W. Yang, J. Chem. Phys., 107, 7921-7925 (1997).
Describing van der Waals Interactions in Diatomic Molecules with Generalized Gradient Approximations: the role of the Exchange Functional .

1. Y. Zhang, G. Wang and Y. Jiang, J. of Nanjing Univ. (Natural Science Edition), 29, 400-406 (1993).
Application of the Faraday Effect in Chemistry.

Last modified: Sep 1, 2021