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Internship Progress (Part 2)

Internship Progress (Part 2). Mahd Nishtar Amanda Ullmer July 9, 2012. Overview . Internship Goal: Identify saccharides in chemical component dictionary. Last Week: Construct queries based on verified protein-based carbohydrate list in Kim Henrick’s list. This Week:

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Internship Progress (Part 2)

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  1. Internship Progress (Part 2) Mahd Nishtar Amanda Ullmer July 9, 2012

  2. Overview • Internship Goal: • Identify saccharides in chemical component dictionary. • Last Week: • Construct queries based on verified protein-based carbohydrate list in Kim Henrick’s list. • This Week: • Modified and tested queries and tabulated results.

  3. Comparison of Kim’s List to Query Results

  4. Furanoses Pyranose • Include: 1 • Exclude: 20 • Include: 1 • Exclude: 20 Ligand Hits: 203 Structure Hits: 544 P & F Ligand Hits: 985 Structure Hits: 6980 • Include: 2 • Exclude: 19 Ligand Hits: 1188 Structure Hits: 7460

  5. Overlapping Results of Ring Structures AHR ALL KDF CNP DA8 DM7

  6. Query Results of Additional Ring Structures KOT 149 1AR MA1 568 NOV

  7. Open Chains • Include: 1 • Exclude: 2 Ligand Hits: 191 Structure Hits: 1379

  8. Overlapping Results of Open-Chain Structures 3MF PAI DER TLA GKR 137

  9. Query Results of Additional Open-Chain Structures 5MM HDL D8T PA5 DGU THE

  10. Statistical Results • Ring Saccharides (Pyranoses and Furanoses): • Total in Kim’s List: 775 • Covered in Kim’s List: 723 • Not Covered: 52 • Extra Query Results: 462 • Sugars: 294 QGA LAG MT7 (obsolete)

  11. Statistical Results Cont’d • Open Chains • Total in Kim’s List: 94 • Covered in Kim’s List: 82 • Not Covered: 12 • Extra Query Results: 109 • Sugars: 32 DRZ (DNA linking) D6P KDP

  12. Exceptions to 5C & 6C Open-Chain Saccharides Kim’s List 3-Carbon Sugars G3H 4-Carbon Sugars DER E4P MRY RES SRT TAR TLA Not in Kim’s List 4-Carbon Sugars DEZ DEA EHM TH6 THE

  13. Ambiguous Structures Kim’s List Query Results KPG GHR NP6 PSX

  14. Next Step… • Clarify ambiguous structures from Kim’s list and from query results. • Design chemical classes for various user scenarios.

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