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20130410 carbohydrates


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The challenges in dealing with sugar stereochemistry

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20130410 carbohydrates

  1. 1. Carbohydrate structurerepresentation and public chemistry databases Colin Batchelor, Ken Karapetyan, David Sharpe, Valery Tkachenko and Antony Williams ACS New Orleans April 2013
  2. 2. OverviewPublic chemistry databases and registrationWhy sugar rings are difficultConsequencesAlgorithmsFuture directions
  3. 3. Some public chemistry databases
  4. 4. How registration worksStructures are accepted in some machine-readableformat and boiled down to some position-independentcanonical form.Drop exact coordinates and retain only relativecoordinates, disregarding bond length.Canonicalization based on depiction of bonds (wedges orhashes) rather than 3D positions around atoms.
  5. 5. Why sugars are difficult
  6. 6. Why sugar rings are difficult
  7. 7. Consequences
  8. 8. Algorithm for hexagons• Identify the perspective conformation (boat, chair, regular hexagon, and so on)• Determine perspective stereo• Assign wedge or hash to the bonds accordingly• (tricky) Reconstruct the sugar ring so as to minimize disruption of the rest of the molecule
  9. 9. Hexagons in the plane
  10. 10. Assigning chair stereochemistryTake the x-axis as either the line through the toptwo ring atoms or bottom two ring atoms.Substituents with Δy positive are up, Δy negativeare down.Then remap chair to a regular hexagon (tricky).
  11. 11. Assigning HaworthstereochemistryThis works for both hexagons andpentagons.Remove any hashes or wedgeswithin the ring.Take the x-axis as a line through one of the ring C–O bonds.Substituents with Δy positive are up, Δy negative are down.The Haworth LLLLLL/RRRRRR hexagon is unappealing, but can be tidiedto a regular hexagon grid without too much disruption.The same goes for the Haworth pentagon.
  12. 12. Future work: integrate with CVSPStructure validation•Warn on query atoms, pseudo atoms, polymers, etc.•Nonsensical stereoAllows users to put together their own standardization workflow usingmodules provided:•Apply default CVSP or user-defined SMIRKS rules•Layout•Neutralize•Get canonical tautomer using ChemAxon’s algorithms•Get biggest organic fragment
  13. 13. More future workImprove chair tidyingDo not disrupt/flip/invert or move around theaglyconeFused ringsRun over all of ChemSpider
  14. 14. Questions?E-mail: