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Effective Strategies for Carbohydrate Substructure Identification and Classification

This guide provides essential tips for the identification and classification of monosaccharides within the Protein Data Bank (PDB). It includes strategies for refining substructure searches, filtering by criteria, and conducting manual analysis. Attention is given to avoiding redundant substructures and ensuring the accuracy of queries. Users are encouraged to understand carbohydrate classifications, including the distinctions between simple and complex C5 and C6 sugars. Additional guidance on utilizing the web interface for exporting data and creating image collages is also included.

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Effective Strategies for Carbohydrate Substructure Identification and Classification

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  1. Carbohydrate Substructure Search Tips Peter Rose June 28, 2012

  2. Identification and Classification of Monosaccharides List of substructures PDB include exclude Refine Substructure Search Color by Substructure Filter by other criteria Manual Analysis

  3. Tips Watch out for stray atoms Avoid redundant substructures Redundant Generic query on the right will match substructure on the left

  4. Tips cont. Test each query separately, even exclusion queries This query does not return Thymidine substructures Try Structure->Clean 2D

  5. Tips cont. Create substructures from existing molecules: example DU 1. Launch chemical structure search from ligand summary page 2. Structure->Aromatic Form-> Convert to Kekule Form 5. Structure-> Clean 2D 4. Structure-> Check structure 3. Delete atoms and stereo bonds

  6. Using the Website effectively • Create image collage of chemical components • Create list of chemical component ids and export as Excel spreadsheet • To create composite lists of multiple queries: • Combine queries with “Match any …”

  7. Strategic Tips Create well-defined subsets of carbohydrates (classification) Stick close to the IUPAC rules • Example: Furanoses • Simple C5 (substituents can only be [H,O,S, Se,…, F, …] and in chains only) • Simple C6 (substituenst can only be [H,O,S, Se,…, F, …] and in chains only) • Complex C5 (generic C5 query excluding Simple C5) • Complex C6 (generic C6 query excluding Simple C6) Complication: A chemical component may match multiple queries, i.e., contains a furanose and pyranose, as well as multiple exclusion queries.

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