Subject: Re: CCL:SCULPT and Chemical Intuition

From: [email-masked] (Mark C. Surles)
Date: Mon, 10 Jul 1995 05:26:03 -0800

Sorry to fill mail queues, but this message was sent to the entire mailing
list and should be addressed publically.

>        Two things I worry about when I hear about programs like
>        SCULPT is :
>
>        1) The "real time" molecular mech. calcs. may be slow for reasonably
>           large systems.

I define "interactive, real time" mechanics as running faster than one
update per second.  SCULPT runs interactively on a 150 MHz R4400 Indigo2
for ~100 residues, and on a four processor challenge for ~370 residues with
neighbor interactions calculated to 10 Angstroms.  Larger structures can
easily be handled by interactively selecting regions of operations.

>        2) The interface seems to rely heavily on "chemical intuition"
>           which often can help you overcome problems, but can just as
>           likely lead you down the garden path. (i.e lead you to false
>           interpretations.)

The results from any molecular mechanics simulations should not be accepted
blindly.  However, there are many properties and interactions that a user
may wish to test which black-box computer algorithms cannot accomplish or
are too cumbersome because they were not designed for the task (e.g. moving
helices to achieve better packing in building models of membrane proteins).

No algorithm should replace a scientists intuition or experience.  SCULPT
provides one more powerful tool to assist scientists in their exploration
and understanding of molecular structure and function.

Mark Surles

>        -Brian
>=============================================================================
>|   .---------.| Brian W. Beck      |    E-mail Addresses:                  |
>|/\ |         ||--------------------|        [email-masked]        |
>|| \\     WSU || Biochem/Biophysics |   [email-masked]                  |
>|\  -        *|| WSU ,  206 Fulmer  |  URL  http://elmo.chem.wsu.edu/~brian |
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