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
- Automatic parametrization of non-polar implicit solvent models for the blind prediction of solvation free energies. J. Chem. Phys., 2016, 145, 124110. Link
- AutoT&T v.2: An Efficient and Versatile Tool for Lead Structure Generation and Optimization. J. Chem. Inf. Model, 2016, 56, 435–453. Link
- 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
- Multiresolution persistent homology for excessively large biomolecular datasets. J. Chem. Phys., 2015, 143, 134103. Link
- Multiresolution Topological Simplification. J. Comp. Biol., 2015, 22, 887-891. Link
- PDB-wide Collection of Binding Data: Current Status of the PDBbind Database. Bioinformatics, 2015, 31, 405-412. Link
- Temperature-Responsive Chiral (A)6B Supramolecular Cages Based on Conformational Preferences. Chem. Asian J., 2015, 11, 465-469. Link
- Target-oriented design and biosynthesis of thiostrepton-derived thiopeptide antibiotics with improved pharmaceutical properties. Org. Chem. Front. 2015, 2, 106-109. (Cover) Link
- Comparative Assessment of Scoring Functions on an Updated Benchmark: I. Compilation of the Test Set, J. Chem. Inf. Model 2014, 54, 1700-1716. Link
- Folding Induces Folding: The Assembly of Aromatic Amide and 1,2,3-Triazole Hybrid Helices. Chem. Eur. J. 2014, 20, 1418-1426. Link
- Chemical and Biochemical Applications of MALDI-TOF MS Based on Analyzing the Small Organic Compounds. Top. Curr. Chem. 2013, 331, 165-192. Link
- Probing the Key Interactions between Human Atg5 and Atg16 Proteins: A Prospective Application of Molecular Modeling. ChemMedChem 2013, 8, 1270-1275. (Back Cover) Link
- 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
- Study on Transient Intermediates in Fast Cyclopropenium-Activated Chlorination Reaction of Alcohols by ESI-MS. J. Mass Spectrom. 2011, 46, 856-858. Link
- Studies on CH3CN-Assisted Decomposition of 1st Grubbs Catalyst by Electrospray Tandem Mass Spectrometry. Rapid Commun. Mass Spectrom. 2011, 25, 3401-3410. Link
- Studies of Heterogeneous/Homogeneous Ion-Molecule Reactions by Ambient Ionization Mass Spectrometry. Curr. Org. Chem. 2011, 15, 3734-3749. Link
- Analysis of Low Molecular Weight Compounds by MALDI-FTICR-MS. J. Chromatogr. B 2011, 879, 1166–1179. Link
- 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
- 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
- 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