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Comprehensive Strategies for Efficient Saccharide Search in Glycobiology Internship

Learn effective methods for identifying saccharides by name, formula, structure, similarity, linkages, and databases. Enhance understanding of saccharide classifications and complexities to improve search accuracy. Utilize essential tools for successful sugar identification.

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Comprehensive Strategies for Efficient Saccharide Search in Glycobiology Internship

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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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