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Internship Progress and Project Summary

Internship Progress and Project Summary. Mahd Nishtar July 2, 2012 Amanda Ullmer . Internship Goals Identify saccharides in chemical component dictionary. Methods Construct queries based on verified protein-based carbohydrate list. Accomplishments

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Internship Progress and Project Summary

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  1. Internship Progress and Project Summary Mahd Nishtar July 2, 2012 Amanda Ullmer

  2. Internship Goals • Identify saccharides in chemical component dictionary. Methods • Construct queries based on verified protein-based carbohydrate list. Accomplishments • Carbohydrates within aminoglycoside antibiotics and Vancomycin-related structures • Classify structures according to saccharide components. • Query assignment • Identify instances of carbohydrate ligands within the PDB.

  3. An Introduction to Carbohydrates

  4. Process: Initial Query Assignment Kim Henrick’s 900+ carb-containing ligands  identified core saccharide structures constructed templates with Marvin Sketch

  5. General Queries:Ring Saccharides Pyranoses Furanoses Q7 Q8 • Constructed general query templates for ring saccharides.

  6. Specific Queries: Ring Saccharides Pyranoses Furanoses Q1 Q2 Q4 Q3 Increasing Specificity Q5 Q6

  7. Open-chain Saccharides Pentanes Butanes Q10 Q9 Q11 Q12 • Constructed specific query templates for open-chain saccharides.

  8. Initial Excluded Structures Ribo-nucleoside (Furanose- Cytosine base) Analogues (Pyranose – Adenine base) Piperidine Abasic Nucleotides

  9. Initial Excluded Structures

  10. Organizing Structure Hits • Excel spreadsheet comparing structure hits between specific ring queries and compiled carbohydrate list (Kim’s list) • Function = ISNA(MATCH(A2,$K$2:$K$732, FALSE)

  11. An Improved Approach

  12. Include Exclude

  13. Organizing Query Templates Compilation of all constructed queries and corresponding MRV files.

  14. Sources • http://cc-tools-1.rutgers.edu/ • http://prd-v3-beta.rutgers.edu/prdmodule/index.html • http://www.rcsb.org/pdb/home/home.do • http://www.chem.qmul.ac.uk/iupac/2carb/cont.html • http://dimitriswin.rcsb.org:8080/pdb • ftp://dimitriswin.rcsb.org/chem_classes

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