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

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Presentation on theme: "Molecular dynamics of two ester hydrolases: comparison using the BioSimGrid database Kaihsu Tai."— Presentation transcript:

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

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

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

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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