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Lily Cheng

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Lily Cheng

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    1. Lily Cheng Beijing, China 07/14/06

    2. Proposed Research

    3. Progress To determine the best binding site and binding energy on ADT. Using ADT, docked and determined the binding energies of 10 conformations for: N1 + DANA, zanamivir, GS4071, and sialic acid. N9 + DANA, GS4071, and FDI. Created an Excel spreadsheet to begin recording binding energies of docking studies. Recorded binding energies of all dockings thus far. The best binding energy yet is around -10 kcal/mol. Investigated docking parameters by reading literature and also by experimenting (changed parameters and observed changes in binding energy). To finish Virtual Screening of N1 (neuraminidase) with NCI Diversity Set. Finished docking receptor modified N1-model from Dong-Qing Wei to the ligand DANA. This will serve as the positive control and the grid files from this docking are used for Virtual Screening. Converted 1,990 NCIDS ligands from pdbq to dlg using a script that Shen Bin wrote. Ranked the ligands by best binding energy and best docking energy. Recorded this data in Excel and created histograms for ligands with negative binding and docking energy. Viewed ligand with best binding energy in ADT; experimented with different grids and molecular maps. To determine if there are new drugs being found by comparison with known drugs. Using the Super Drug Database (SDD) and RCSB, compiled a list of drugs with structures similar to zanamivir, oseltamivir and sialic acid. From PubMed and RCSB, researched papers written on potential new drugs and/or the drug discovery process using molecular docking. VTC with Wilfred postponed to Week 4 due to Dr. Lu and Shen Bin being away this week.

    4. Plans To continue to analyze the results of the Virtual Screening of the NCIDS using the modified N1-model as receptor. Generate pictures of the hydrogen bonding, hydrophobic and hydrophilic interactions of the top 10 ligands with the receptor. Read the LIGPLOT manual; figure out how to use LIGPLOT. If it is not possible to generate clear pictures on ADT, use LIGPLOT to do visualization of ligand-receptor binding. To do Virtual Screening with the ZINC database. Obtain pdb or pdbq copies of the ligands in the ZINC database. Learn to submit jobs to be run on the network. Analyze the results of Virtual Screening with the ZINC database. To continue to write the background, materials/methods for the research paper. VTC with Wilfred.

    5. Photo

    6. Notes We had an earthquake! I am unsure if the N1 model, after being modified extensively, is still a good representation of the native N1 binding site. While the two modified residues were not directly in the binding site, the many deleted lone pairs might have had an effect on binding.

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