关于我


不积跬步,无以至千里;不积小流,无以成江海。 – 荀子

自我简介 / About Me

     业余编程爱好者, 喜欢折腾各种程序和系统. 主业是计算机辅助药物设计研究人员, 从事计算生物学, 计算化学, 化学信息和生物信息等相关研究. 研究兴趣是改进药物设计计算算法, 提高辅助模拟可靠性, 使计算在科学中得到更多应用, 而不是戴着”马后炮”的帽子.

     因为涉及的东东比较广, 脑袋实在不够用, 在这里作记录和分享, 希望能帮到大家啦!~ 因其实质是个个人在线笔记本, 记东西比较乱, 也没有太多时间整理, 希望不要介意~ 欢迎提供宝贵意见 comments 或者给我mail: zhaozxcpu(at)hotmail.com !

     下年等基金申请过后上课以后闲下来, 打算用比较fancy的js来重造博客界面. 希望有时间吧.

Some Tools I developed:

  • MIBPB webserver: automatic online server based on matched interface PB solver to calculate electrostatic solvation energy, ESES/MSMS surface, structure preparation and residue pKa calculation.
  • AutoT&T2 and PG-AutoT&T: Fragment-based lead optimization tool. AutoT&T speeding up and new pharmacophore guided optimization/de novo design.
  • AutoPhD (Pharmacophore Deduction): Pharmacophore perception for ligand/protein or protein/protein complex.

Publications

  1. Automatic parametrization of non-polar implicit solvent models for the blind prediction of solvation free energies. J. Chem. Phys., 2016, 145, 124110. Link
  2. AutoT&T v.2: An Efficient and Versatile Tool for Lead Structure Generation and Optimization. J. Chem. Inf. Model, 2016, 56, 435–453. Link
  3. Enzyme-Dependent [4 + 2] Cycloaddition Depends on Lid-like Interaction of the N-Terminal Sequence with the Catalytic Core in PyrI4. Cell Chemical Biology, 2016, 23, 1–9. Link
  4. Multiresolution persistent homology for excessively large biomolecular datasets. J. Chem. Phys., 2015, 143, 134103. Link
  5. Multiresolution Topological Simplification. J. Comp. Biol., 2015, 22, 887-891. Link
  6. PDB-wide Collection of Binding Data: Current Status of the PDBbind Database. Bioinformatics, 2015, 31, 405-412. Link
  7. Temperature-Responsive Chiral (A)6B Supramolecular Cages Based on Conformational Preferences. Chem. Asian J., 2015, 11, 465-469. Link
  8. Target-oriented design and biosynthesis of thiostrepton-derived thiopeptide antibiotics with improved pharmaceutical properties. Org. Chem. Front. 2015, 2, 106-109. (Cover) Link
  9. Comparative Assessment of Scoring Functions on an Updated Benchmark: I. Compilation of the Test Set, J. Chem. Inf. Model 2014, 54, 1700-1716. Link
  10. Folding Induces Folding: The Assembly of Aromatic Amide and 1,2,3-Triazole Hybrid Helices. Chem. Eur. J. 2014, 20, 1418-1426. Link
  11. Chemical and Biochemical Applications of MALDI-TOF MS Based on Analyzing the Small Organic Compounds. Top. Curr. Chem. 2013, 331, 165-192. Link
  12. Probing the Key Interactions between Human Atg5 and Atg16 Proteins: A Prospective Application of Molecular Modeling. ChemMedChem 2013, 8, 1270-1275. (Back Cover) Link
  13. Self-Resistance to an Antitumor Antibiotic: A DNA Glycosylase Triggers the Base-Excision Repair System in Yatakemycin Biosynthesis. Angew. Chem. Int. Ed. 2012, 51, 10532-10536. Link
  14. Study on Transient Intermediates in Fast Cyclopropenium-Activated Chlorination Reaction of Alcohols by ESI-MS. J. Mass Spectrom. 2011, 46, 856-858. Link
  15. Studies on CH3CN-Assisted Decomposition of 1st Grubbs Catalyst by Electrospray Tandem Mass Spectrometry. Rapid Commun. Mass Spectrom. 2011, 25, 3401-3410. Link
  16. Studies of Heterogeneous/Homogeneous Ion-Molecule Reactions by Ambient Ionization Mass Spectrometry. Curr. Org. Chem. 2011, 15, 3734-3749. Link
  17. Analysis of Low Molecular Weight Compounds by MALDI-FTICR-MS. J. Chromatogr. B 2011, 879, 1166–1179. Link
  18. Gas-phase Synthesis of Hydrodiphenylcyclopropenylium via Nonclassical Favorskii Rearrangement from Alkali-cationized α,α′-dibromodibenzyl Ketone. Rapid Commun. Mass Spectrom. 2010, 24, 2665-2672. Link
  19. Studies of the Interesting Gas-Phase Rearrangement Reactions of 2-Pyrimidinyloxy-N-arylbenzylurea Promoted by Urea-Carbaminidic Acid Tautomerism by ESI-MS/MS and Theoretical Computation. Chin. J. Chem. 2010, 28, 1765-1772. Link
  20. Progress in ESI-MS Study for the Catalytic Asymmetric Reactions. Chinese J. Org. Chem. 2010, 30, 809-815. Link

Hobbies

  • Chinese food (Spicy better)!! Sweet chocolate, cake, candy!!
  • IT and Computers, Electronics
  • Sports: Swimming, Tennis, Running
  • Watch matches for: American Football, Tennis, NBA, European Football (Barcelona)
  • Fan for: MSU, Roger Federar, Argentina football and Messi, Hengda football

Skills

Computational Biology/Chemistry:

  • Molecular Modeling (Docking, Virtual Screening, Pharmacophore, Structure Modeling, CADD, QSAR) with MOE, Schrodinger, SYBYL, Discovery Studio, Gold, Autodock, Modeller et al.
  • MD simulation with Amber, NAMD2, Desmond.
  • QM and QM/MM with Gaussian for optimization/TS/IRC.
  • Visualization with Pymol, Chimera, VMD, JSmol

Programmer

  • Daily tasks and system administration: Bash(4yr), Python(3yr)
  • Program development: C++(2yr)
  • Numerical Computation: Fortran(1yr), Matlab(1yr), R(1m)
  • Website: HTML/CSS(0.5yr), PHP(0.5yr), JS(0.5yr), MySQL(0.5yr)
  • IDE: Sublime, Eclipse, VS, Notepad++
  • Writting: Markdown, Latex, Endnote
  • Other: Git,

Chemist

  • Organic Mass Spectrometry focusing on ESI-MS/MS (2yr)
  • Organic Synthesis (3yr)
  • NMR analysis (1yr)
  • Fluorescence Polarization (FP) for peptide/protein binding(0.5yr).

Places I have been to

  • Foshan (My lovely hometown)
  • Nanjing (My undergraduated student life)
  • Shanghai (Best place in China, graduated student life)
  • East Lansing (Quiet town for my postdoc study)
  • Guangzhou, Shenzhen, Wuhan, Ningbo, Suzhou, Wuxi, Qingdao
  • Detroit, Minneapolis, Chicago, Toronto, Boston, New York, Washington DC, Philadelphia, Lancaster, Columbus, San Francisco, San Jose, Monterey, Berkeley, Santa Barbara, San Diego, Los Angeles, Las Vegas, Santa Monica

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