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Molecular dynamics of two ester hydrolases: comparison using the BioSimGrid database

Molecular dynamics of two ester hydrolases: comparison using the BioSimGrid database. Kaihsu Tai. H142. S144. N156. S203. H447. E334. OMPLA. AChE. The systems. both serine esterases (ester hydrolases, EC 3.1.1) with the catalytic triad: Ser - His - Glu|Asn. The trajectories.

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Molecular dynamics of two ester hydrolases: comparison using the BioSimGrid database

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  1. Molecular dynamics of two ester hydrolases: comparison using the BioSimGrid database Kaihsu Tai

  2. H142 S144 N156 S203 H447 E334 OMPLA AChE The systems • both serine esterases (ester hydrolases, EC 3.1.1) • with the catalytic triad: Ser - His - Glu|Asn

  3. The trajectories

  4. ...not yet data deluge • but...

  5. articles with “molecular dynamics” in title or abstract in the Biophysical Journal (one of the first protein MD: 1980 McCammon et al.)

  6. Things we tried that did not work very well • Picking candidate atoms from the side chain of the triad and generate • the meta-plot • the meta-histogram

  7. Meta-plot

  8. Meta-histogram

  9. A set of metrics for triad intactness

  10. A set of metrics for triad intactness

  11. Looking ahead • Here we had some intuition, and formed a model. • Is it possible to do model-free data mining? • n × n rmsd (as Bing may have shown), etc. • Yes, we can do it, but what is the biological/biochemical relevance? • The answer is 42 - what is the question?

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