IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

Some questions

Holger Scheib hscheib at tebio1.biologie.uni-stuttgart.de
Thu Apr 10 06:00:22 EST 1997

Dear collegues,

my name is Holger Scheib and I am working at the Institute of Technical
Biochemistry at the University of Stuttgart, Germany. Recently, we decided to
get your Grasp software which is a real nice and handy tool and well suited for
my research interests.
I am investigating lipase-triglyceride complexes and would like to calculate
1st the total accessible surface and 2nd the accessible surface for polar as
well as for hydrophobic amino acid residues.
So far, I performed several calculations leading to the following results:

total surface            unpolar surface                  polar surface
11007 (4220)             3548 (1721)                      3434 (1434)
11002 (4220)             3519 (1721)                      3551 (1434)
10945 (4220)             3540 (1721)                      3463 (1434)
11086 (4220)             3554 (1721)                      3454 (1434)

The values on the left of each column are the surface sizes in squared
angstroems. The values in brackets represent the number of atoms that have been
considered for the surface calculation. I performed the calculations as
mentioned in your Manual.
Here my questions in detail:

Why isn't the accessible total surface the sum of accessible polar and unpolar
surface? Or why are roughly 1000 atoms ignored for these calculations? What
happens to the rest?

Are Hydrogens used for the calculation of a surface or will Grasp sort them out
before calculating the surface?

Is the accessible surface calculated from the center of the (standard) 1.4 A
probe or from the probe surface?

Are substrate VdW radii automatically set or accepted by Grasp or will I have
to manually adding them to some file?

Is there a possibility to color the surface by hydrophobicity?

It would be great to hear from you soon.
Thanx a bunch in advance.


* Dipl. Chem. M. Sc. Holger Scheib                    *
* Institut fuer Technische Biochemie                  *
* Universitaet Stuttgart                              *
* Allmandring 31                                      *
* 70569 Stuttgart                                     *                           
*                                                     *
* Tel.:  (0711) 685-7481                              *
* Fax.:  (0711) 685-3196                              *                          * email: hscheib at tebio1.biologie.uni-stuttgart.de     *
* www: http://www.itb.uni-stuttgart.de:8080/home.html *

More information about the Bio-soft mailing list

Send comments to us at archive@iubioarchive.bio.net