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CADD Project Report

CADD Project Report. 學號 : 姓名 :. http://gemdock.life.nctu.edu.tw/dock/download.php. Target Protein. Compounds 990. 2. 0. 2. 1. 0. Test Set : 990 Ligands. ZINC Database. Ligand : pdb1aaq_PSI.mol. Protein: cav1aaq_PSI.pdb. +. 5. 4. 9. iGemDock (Standard). Rank: 3 /991.

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CADD Project Report

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  1. CADD Project Report 學號: 姓名:

  2. http://gemdock.life.nctu.edu.tw/dock/download.php Target Protein Compounds 990

  3. 2 0 2 1 0 Test Set : 990 Ligands ZINC Database Ligand : pdb1aaq_PSI.mol Protein: cav1aaq_PSI.pdb + 5 4 9 iGemDock (Standard) Rank: 3/991 Similar Compound Search (Tanimoto-60) 8 991 Docked Pose 10 compounds Top 15 Compounds 10 11 12 13 14 6 SiMMap iGemDock (Accurate) 7 Anchors Top 5 Compounds PDB Post-screening Analysis Docking Pocket Analysis(PyMol) 3 Conclusion Mechanism of Drug Actions

  4. Target Protein and Ligand 0 4dfr MTX

  5. Introduction of Target Protein 1 • What is this protein? (from paper) • How many chains? • Please show the secondary structure. • Are there any disulfide bonds? 4dfr

  6. NMDA receptors are the Glutamate receptor ionotropic

  7. 指令： color by chain 兩種顏色代表含有兩條chain A chain：green B chain：blue

  8. 針對A、B chain 紅色代表 a-helix (共含有17條) 黃色代表 b-sheet(共含有29條) 綠色代表 loop (共含有42條)

  9. Disulfide bonds

  10. Ligand present 2 GLU C5 H9 N O4

  11. Mechanism of Drug Actions 3 Nature vol 438|10 Nov. 2005|doi:10.1038/nature04089

  12. Nature vol 438|10 Nov. 2005|doi:10.1038/nature04089

  13. Molecular Docking Using iGEMDOCK 4 Standard Docking

  14. Rank 5

  15. SiMMap 6

  16. SiMMap Anchors 7 G186 G185 V1 E1 PLP F55 R135 MLI E2 K56

  17. Top15 Compounds from 990 set 8

  18. Similar Compound Search 9 Tanimoto-60

  19. 10 10 Compounds from similarity search 1 2 3 4

  20. 10 6 7 9 5 8

  21. Molecular Docking Using iGEMDOCK 11 Accurate Docking

  22. Post-screening Analysis 12 • Table of Docking Energy • Figure of Docking Energy • Interaction Profile • Interaction Analysis

  23. Table of Docking Energy

  24. Figure of Docking Energy 1 3 5 2 4 Energy Compound

  25. Interaction Profile of Top5

  26. Interaction Analysis of Top5 • 紅色部分是指靠電子吸引的鍵結 • 綠色部分是指靠氫鍵的鍵結 • 灰色部分是指靠凡得瓦力的鍵結

  27. G186 Top1 G185 13 V1 E1 F55 4-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)-4-pyridyl]methyleneamino]butanoic E2 R135 K56 ZINC20113196

  28. G186 Top2 G185 V1 E1 F55 4-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)-4-pyridyl]methyleneamino]butanoic E2 R135 K56 ZINC20113196

  29. G186 Top3 G185 V1 E1 F55 4-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)-4-pyridyl]methyleneamino]butanoic E2 R135 K56 ZINC20113196

  30. G186 Top4 G185 V1 E1 F55 4-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)-4-pyridyl]methyleneamino]butanoic E2 R135 K56 ZINC20113196

  31. G186 Top5 G185 V1 E1 F55 4-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)-4-pyridyl]methyleneamino]butanoic E2 R135 K56 ZINC20113196

  32. Conclusion 14

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