I've made the analysis of resulted structures with Molprobity server (Ramchandran etc.).
They have some deviations from limits and ideal values. I wonder if I need to make a local minimization for them in the explicit solvent. Or probably this is not required, because protein structure probably can't be ideal in dynamic conditions because of solvent infuence. I even don't mention induced fit by the ligand.
Best regards,
Andrew
06.12.09, 10:23, "Thomas Cheatham" <tec3.utah.edu>:
>
> > Yes, larger motions have some influence as far as the binding site is in
> > the interface of homodimer and there are some little oscillations in
> > monomers distance. But I actually also want to optimize somehow the
> > number of clusters.
>
> You can read our paper on clustering MD trajectories in JCTC (Shao et al.)
> and from this you will see that the metrics are not always so clear. In
> practice, my general path is to look at a 2D RMSd plot and count the
> number of big squares on the diagonal. Alternatively, I look at the
> cluster counts (i.e. how many frames in each cluster) which is reported at
> the bottom on the *.txt file... i.e. below it looks like there are 4
> major clusters (1, 2, 5, 6) based on the count; the graphical time course
> suggests that the clusters are not revisited much...
>
> #Clustering: divide 258425 points into 7 clusters
> #Cluster 0: has 6647 points, occurence 0.026
> #Cluster 1: has 133732 points, occurence 0.517
> #Cluster 2: has 58864 points, occurence 0.228
> #Cluster 3: has 243 points, occurence 0.001
> #Cluster 4: has 1110 points, occurence 0.004
> #Cluster 5: has 32013 points, occurence 0.124
> #Cluster 6: has 25816 points, occurence 0.100
> #Cluster 0 . ... .. . . . 54.1 . ....
> #Cluster 1 9XX999X99XXX999999X9X9X98. . .....54.. .. ..
> #Cluster 2 . ...... . . .1999999799994...
> #Cluster 3 . ....... .
> #Cluster 4 .1.
> #Cluster 5 . .. .5781...29997
> #Cluster 6 ..89997 ..2
>
> -- tec3
>
>
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Received on Mon Jan 04 2010 - 14:00:02 PST
