Subject: Re: CCL:cavity volume calculation

From: Craig Taverner <[email-masked]>
Date: Wed, 22 Nov 1995 15:59:37 +0200 (GMT+0200)

Hi Qu,

> I am studying on the thermostability of 3-isopropylmalate dehydrogenase. 
> Protein engineering showed that at a certain site, Ala-->Leu mutation 
> increased the stability of protein. Crystallography analysis showed that the 
> sidechain of Leucine reduced the cavity around mutation site. Although the
> dot surface illustration can show this point very well, we are asked to give 
> the cavity volume in each case. However, we have no such a program. Could you 
> help me? Thanks in advance.

I have a program to calculate various steric effects in molecules and 
crystals, and recently added a cavity volume calculation to it for the 
calculation of the cavity volume in the region of perchlorate groups in 
crystals.  The main way of calculating the cavity volume is using a Monte 
Carlo sampling approach, which gives very fast results, with moderate 
accuracy.  There are four different cavity volumes calculated, depending 
on exactly what is meant by cavity volume (depends mainly on how you 
define the boundry to the cavity).  Unfortunately the program does not 
yet include a cavity search algorithm, so you have to tell it exactly 
where the cavity is.

If you're interested, the program is available at:
ftp://hobbes.gh.wits.ac.za/pub/steric/steric_1.08.tgz

There is a readme file for installation info, and online help, but I'd 
recommend you e-mail me for specific info, particularly about the cavity 
volume calculation, because it's quite a new addition to the program.  
The program was developed under linux unix, but has been compiled on 
several other unix's with small changes to the Makefile.

Cheers, Craig

"If God had meant us to be naked, we would have been born that way."

Craig Taverner
Structural Chemistry, University of the Witwatersrand, South Africa

---

From: [email-masked] (C.S.RAMAN)
Date: Wed, 22 Nov 1995 18:09:28 -0600 (CST)

> help me? Thanks in advance.

In my opinion, the best program to do volume calculations on
Protein structures is that written by Fred Richards (Yale U.) called
VOLUME.  It employs the Voronoi method to accomplish the volume
calculations.  You can obtain the source from Patrick Fleming:
[email-masked]. It can be compiled with ease on any Unix platform.

Cheers
-raman
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