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Strategies for Saccharide Searching

Strategies for Saccharide Searching. Summer Interns Jun. 24, 2011. Search by Name. From figure in Glycobiology textbook chapter 2 From Google search for sugars Filter results visually and by name Undecided about some components since saccharide identification rules not clear Action item:

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Strategies for Saccharide Searching

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  1. Strategies for Saccharide Searching Summer Interns Jun. 24, 2011

  2. Search by Name • From figure in Glycobiology textbook chapter 2 • From Google search for sugars • Filter results visually and by name • Undecided about some components since saccharide identification rules not clear • Action item: • Complete search by name (starting from natural sugars) • Get a clearer understand of saccharide classifications

  3. Fischer projections of the acyclic forms of the D series of aldoses FIGURE 2.3. Fischer projections of the acyclic forms of the D series of aldoses, ranging from triose to hexose. Essentials of Glycobiology Chapter 2, Figure 3 Second Edition

  4. Search by Formula • Variations of (CH2O)n • Weed out the non-sugar components by visual analysis and names • Action item: • Need to do this a little systematically and completely

  5. Search by matching to a structure • Start with the 6 member ring with C5 and O1 • Repeat with cases where the O is replaced by S (thio-sugars) or N (Aza-sugars) • Challenge is that there are some really wired cases where it is not clear what to do • Action item: • Classify the ones that are obvious and go back to the doubtful cases later

  6. Search by Similarity • Once a set of basic sugars have been identified, search the CCD for similar smiles, substructure searches etc. • Use the PDBe services to find structures that have pyranoses and furanoses (see slides from Kim) also try to search more by structures

  7. Search based on linkages • Searching for entries in the PDB by linkages would be useful but was not readily doable at this stage. • Check for information from the functional Glycomics website – not easy to understand their data • Action Item: • Look for MODRES “Glycosylation” records in files and find the sugars attached to the proteins by looking through the link records

  8. Based on other Databases • Monosaccaride DB • Has only 367 sugars • Action Item: • Max will look into downloading these and checking for them in the CCD • Functional Glycomics • Not clear how to use this

  9. Other practical details -1 • Google docs lists: • Max has set up a list for sharing and consolidating the saccharides lists • Max periodically cleans up the list to remove duplications • Get only CC ID – other details like, name, formula, image etc. can be pulled up as needed • “Is it a saccharide?”: Max wants to create a gameto rapidly check through the lists of saccharides • SD/JW: Remember to use remediation sandbox when loading files into the mini DB at RU

  10. Other practical details - 2 • Students (Aileen) summarized questions. SD sent them to KH • Students need to keep a log of the queries that they are running so that they can be redone later to catch all new sugars and sugar containing entries.

  11. Other Matters?

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