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Re: Loop Modeling

Hi, Andras

Thanks for the information.

I anticipated your answer, and did a cluster analysis on the loops RMDS. One of the loop structures (12-resiude) was way-out, but all the others seemed to fall into one of two possible clusters of stuctures. However, it may be that I was asking a different question.

One thing. I did the aligning and RMSD measurements using Swiss-PdbViwer (Deep View) as that allowed me to align the structures by selected residues and measure the RMSD of other selected residues. Can this be done using Modeller (Deep View has some limitations). MALIGN3D and COMPARE appear only to act on complete structures (but I may be wrong).

About the 6-10 hours running time on Mac OS X / Darwin. This may be due to the computational overhead of running OS X - perhaps if it were run in the console mode, things may be faster. However, an overnight run is not a problem. Luckily, the time factor is not a problem (at the moment) as I am doing all this in my spare time, trying to learn some protein modelling. I'll have to ease off a bit as I'm about to start a second year of a part-time MSc (Structural Molecular Biology) at Birkbeck. No more spare time.


Alex Brown

On Wednesday, November 6, 2002, at 05:45  pm, Andras Fiser wrote:

hi Alex,

a few points:

we used this approach to enforce our confidence in predicting of a 6 res
segment and explore the possible uncertainty in the environment. I.e.
the analysis was aiming to explore the question, how far one can extend
selecting the loop environment and still predicting a similar
conformation? since the conclusion was, that the shorter loops (6, 7N,
7C, 8N 8C .. )are returning the same conformation and at some loop
length it got drastically worse (random)  any of those shorter
consistent loops will be suitable for a final model.
 Unfortunately the details of this extensive study are not published,
just a short report about reinforcing our prediction with NMR data and
vice versa for this special case.

More importantly: Modeller scores are -essentially- a cumulative summary
of the restraints deviations in a probabilistic form. Conversely the
scores depend on the set of restraints selected, which is directly
correlated with  the number of atoms involved. It means that scores can
be compared if you select the same loop to optimize but not among
different loops. I.e. the scores from separate  modeling of 6,7,8.. res
long loops are not comparable.

Once the best loop  or a couple of best loops are selected energetically
(i.e. modeller score-wise) from each loop prediction (same loop selected
for optimization), these "best" loops from different sets of loop
prediction (involving different loop lengths)  were compared
geometrically, (RMS-wise) for consistency.

another note: 6-10 hour sounds slow even if you use  one computer only.
We used SGI unix and red hat linux on pc, maybe the  MAC OS is not
optimal for this.  Normally one loop optimization is around 1 minute  or
so,  i.e. 200 runs is ~2+ hours. But it maybe normal given the compiler
and code optimization differences among various platforms. However I
would expect that a computational lab has more than 1 processor: if you
submit them in parallel to several machine you can drastically reduce
the time required for these calculation. E.g.  in our case we can
conduct a calculation like this in 1 minute. The only parameter you need
to set differently in each loop top file is the random number seed


Andras Fiser, PhD            # phone: (212) 327 7216
The Rockefeller University   # fax:   (212) 327 7540
Box 270, 1230 York Avenue    # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras