Antibody 3D Modeling

Andrew Martin martin at bsm.bioc.ucl.ac.uk
Thu Nov 3 06:32:45 EST 1994

Hiroyoshi Ohba (ohba at YL05HP.TB.NODA.SUT.AC.JP) wrote:

: HELLO Netters;

:         Is there any software which assembles three-dimesional structure of
: antibody Fab?   Now, I am not familier with structural biology but like to
: analyse the effect of molecular modification of antibody.  I have tried AbM
: of Oxford Molecular Ltd which has been developed by Prof. Tony Rees's Lab.
: It works on the stand-alone Silicon Graphics and HP workstations. In my
: case on assembling human Fab from its amino-acid sequence, enormous time
: (days) was required for caliculation.  Would you suggest quicker softwares
: on faster machines, or software employing other argorisms?  All of your
: comments are welcomed.
Hi Hiroyoshi,

I'm the original author of the academic version of the AbM package while I
was working in Tony's lab. in Oxford before he moved to Bath. Andrew Henry's
comments are all pretty valid; you can make a crude model quickly, but you
have to make a trade-off between time and quality of the model. With longer
loops once will always have problems, whatever method is employed; the
structural database is not really saturated for loops longer than about
7 amino acids while conformational search methods take *really* long times
for longer loops (a full conf. search of a 17 residue loop would take
around 250000 years on something like an Indy!!!) AbM therefore makes
a tradeoff of using the database to build most of the loop, but reconstructing
a small section (by default the middle of the loop, but you can choose)
which yo think is most likely to be involved in antigen interactions or
surrounding a mutation site.

I really don't think there is a better way of doing things at present,
but I'm working on it!!


Dr. Andrew C.R. Martin,         University College London & SciTech Software
INTERNET: martin at bsm.bioc.ucl.ac.uk      Tel: (Work) +44(0)71 387 7050 X3284
JANET:    martin at uk.ac.ucl.bioc.bsm           (Home) +44(0)372 275775

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