Presentation on theme: "Molecular dynamics of two ester hydrolases: comparison using the BioSimGrid database Kaihsu Tai."— Presentation transcript:
Molecular dynamics of two ester hydrolases: comparison using the BioSimGrid database Kaihsu Tai
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
●...not yet data deluge ● but...
articles with “molecular dynamics” in title or abstract in the Biophysical Journal (one of the first protein MD: 1980 McCammon et al.)
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
A set of metrics for triad intactness
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?