Subject: SUMMARY: Superposing 2 MoleculesB

From: "C.F. Matta" <[email-masked]>
Date: Fri, 17 Dec 1999 12:09:45 -0500 (EST)

Hi everybody

A couple of weeks ago I posted the following question:

     "Is there a free (or inexpensive) software to superimpose a floppy
     structure (F) on a rigid template structure (R).  The objective is to
     obtain a geometry of (F) in a conformation that mimic (R) as closely
     as possible (in a least square sense)."

I got the replies, form:

G. Matthias Ullman, Per-Ola Norrby, Christian Rummey, Nick Jewell,
Alexander Klinsky Gregory Durst, Thomas E. Wiese, Soaring Bear, and
Dayong He  

which are very much appreciated. G. Matthias Ullman has a C code that he
generously sent, and for which I am very greatful.

Here are the replies:

---------------------REPLY 1-------------------------------------------

I have some code in C that does the job using the Kabsch-Algorithm. you may
however have to modify it. If you don't find anything better, let me know.

Matthias

G. Matthias Ullmann
Department of Molecular Biology
The Scripps Research Institute
10550 N. Torrey Pines Rd., TPC-15
La Jolla, CA 92037 USA
Phone:  858-784-8889
Fax:    858-784-8896
e-mail: [email-masked]
www:    http://www.scripps.edu/~ullmann

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---------------------REPLY 2-------------------------------------------

	You can do that with MacroModel.  It's not free, but if you're
academic it's relatively inexpensive.  Check out:
http://www.schrodinger.com/macromodel2.html
You can specify which atoms in both molecules to overlap, and what torsions
to rotate.  We use it for testing pharmacophore hypotheses.  Two drawbacks
with this procedure: there is no "global best fit" finding, so you have to
check through several possible overlap conformations, and there is no
possibility to bias the fit against high energy structures.  On the other
hand, MacroModel includes a good set of conformational searching and
constrained minimization tools, which can frequently be applied to the same
kind of problems.

	Best regards,

	Per-Ola Norrby

* Per-Ola Norrby, Dept. of Med. Chem., Danish School of Pharm.
* [email-masked], http://compchem.dfh.dk/PeO/
* tel. +45-35306506, fax +45-35306040

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---------------------REPLY 3-------------------------------------------

I attach a tar file with the code. There is a very short README file how to use
it and two examples. I hope you figure out what to do and how to modify the
program for your need. Please let me know if you need more help. But I am very
busy right now, writing papers and proposals. (That's the reason why I am still
here :-). Large parts of the code I send you are "dead". You should be only
interested in my-kabsch.c and in superimp.c.

Have fun,

Matthias

G. Matthias Ullmann
Department of Molecular Biology
The Scripps Research Institute
10550 N. Torrey Pines Rd., TPC-15
La Jolla, CA 92037 USA

Phone:  858-784-8889
Fax:    858-784-8896
e-mail: [email-masked]
www:    http://www.scripps.edu/~ullmann

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---------------------REPLY 4-------------------------------------------

there is a (in the meantime comercial, sold by Tripos) programm doing
exactly this. If it is no option for you to buy it (it is part of the
programm package SYBYL), you should at least look at

C. Lemmen, T. Lengauer, J. Comput.-aided Molecular Design, 11 (1997)
357-368.

I can send you a postscript-file of it if you wish. I obtained the
programm itself ("FLEXS") from The GMD (cartan.gmd.de) when it was in
test phase. Maybe it can still be obtained from there.

I am very interested in the alternatives !

--cr

Christian Rummey, Dipl. Chem.
Institut fuer Organische Chemie, Universitaet Wuerzburg
mailto:[email-masked]
registered linux user #92917

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---------------------REPLY 5-------------------------------------------

There are a number of alignment methods you could try, for example: the SEAL
code is often available through this
group (as Fortran 77 code) and there's FlexS
(http://cartan.gmd.de/flex-bin/FlexS) which allows you to either procure a
license from the authors or have quite a few 'free tries' through allocation
at their web site. In our group at Sheffield we have the Field Based
Similarity Searcher (FBSS) which uses a GA to align molecular fields,
although the flexibility issue is still a problem within the code, and is
more useful for rigid fitting. If you have SYBYL, there are superposition
procedures in this program, including SUPERIMPOSE and FIELD_FIT, but I
understand that this program is relatively expensive(!)

Hope this helps,

Nick Jewell

Research Student
Department of Information Studies
University of Sheffield
Sheffield, UK

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---------------------REPLY 6-------------------------------------------

There is a program named SEAL which does what you want. It was distributed
with the original paper and is obtainable via QCPE. 

On a PC you can download a 30-day trial of powerfit from
www.microsimulations.com. This uses also the SEAL algorithm but comes with
a graphical user interface.

In April 99 there was a paper from the same authors  of SEAL about a new
approach called SQ (J. Med. Chem) but i ewas not able to test this program
up to this time.

Kind regards, Alexander Klinsky
Inst. of theoretical chemistry
Univ. of Vienna
Austria

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---------------------REPLY 7-------------------------------------------

An inexpensive piece of software to do superimposing is SEAL from QCPE in
Bloomington, IN, USA. It requires the ability to read Sybyl mol2 files to
visualize. (Babel could probably convert these to other formats). SEAL is no.
QCPE-634.  Check out the QCPE web page at:
http://www.ccl.net/ccl/qcpe/QCPE2/index.html

regards,
Greg
+-----------------------------------------------------------+
| Gregory L. Durst                  computational chemist   |
| Lilly Research Laboratories       tele: 317/433-3386      |
| Lilly Corporate Center            email: [email-masked] |
| Indianapolis, IN 46285   USA                              |
+-----------------------------------------------------------+

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---------------------REPLY 8-------------------------------------------

I have just done an evaluation of FlexS and it seems to be very 
useful.  I also found that it can be run from within sybyl (with 
special interface).  Since we have sybyl, I will purchase it from 
Tripos Assoc (~$1500).

For FlexS info : http://cartan.gmd.de/flex-bin/FlexS

For sybyl info (no info on FlexS yet, but you can call them): 
http://www.tripos.com/

Good luck,

Tom Wiese

Thomas E. Wiese, Ph.D.

Assistant Professor of Biochemistry
Division of Basic Pharmaceutical Sciences
College of Pharmacy
Xavier University of Louisiana
7325 Palmetto St
New Orleans, LA  70125-1098
Email: [email-masked]
Phone: (504) 483-7433
FAX: (504) 485-7930

Assistant Professor
Department of Environmental Health Sciences (SL-29)
School of Public Health and Tropical Medicine
Tulane University Medical Center
1430 Tulane Avenue
New Orleans, LA  70112-2699
Email: [email-masked]
Phone: (504) 988-6376
FAX: (504) 585-6428

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---------------------REPLY 9-------------------------------------------

	REPLY TO A SIMILAR QUESTION IN THE PAST
        =======================================
	Subject: CCL:Summary :Superimposition Program

I am not sure if this helps; but did you take a look at swisspdb viewer
http://www.expasy.ch
Dr. Y. U. Sasidhar, Associate Professor, Department of Chemistry
Indian Institute of Technology, Powai, Mumbai 400 076, INDIA
----------

  You can use the CCP4 program PolyPose for the purpose. If you don't have
CCP4 (which, I believe you don't). You can use Gerard's program LSQMAN
which is the most versatile superimposition program I've seen, but
requires some inspired script writing. Lastly I've got a fast
superimposer, which is a debugged and improved version of the one I wrote
in Pune.
  For more info. see the following:
LSQMAN http://alpha2.bmc.uu.se/~gerard/manuals/lsqman_man.html

CCP4 (PolyPose and many other useful programs)
http://www/dl.ac.uk/CCP/CCP4/main.html

super_duper.c  (That's mine)
Can superimpose using the whole molecule or any sub-set which you
define. The algo. is the same as the one I wrote in Pune, but now
re-written and de-bugged. I can send you OSF1 Version 4.0 (DEC-ALPHA)
executable, or the C-sources. Finally if you want any special things
to be done, it may be possible to incorporate them.

Devapriya Choudhury

Office:                           Home:
Deptt. of Molecular Biology       Oskar Arpis Vag 2,2
Box 590, BMC,                     S75650, Uppsala
S75124, Uppsala                   Sweden
Sweden
e-mail [email-masked]

-----------

it's called profit and does exactly what ou want!

        cheers,
        gerald

Gerald Loeffler - Bioinformatics Scientist
Boehringer Ingelheim R&D Vienna, Molecular Biology Department
Email: [email-masked]

----------

You may try the molecular modelling package MOLMOL from ETH Zuerich.
It is a graphical program which can also be run in batch-mode (without
graphics-display.
It can be controlled from shellscripts or directly at the commandline.
It is able to superimpose as many molecules as you wish in several modes
(to first, to mean, circular), and you can choose, which atoms or
residues to consider for superposition.
It is freeware!
Take a look at http://www.mol.biol.ethz.ch/wuthrich/software/molmol/
There are versions for UNIX (IRIX, DEC OSF, SOLARIS, LINUX), VMS, and
Windows95/NT. You can also get the source and adapt it to whatever you
want.

Marc Saric

Lehrstuhl fuer Biophysik
Projektgruppe Theoretische Biophysik
http://www.bph.ruhr-uni-bochum.de/
Ruhr-Universitaet Bochum
Germany

----------

Try MOLMOL:
There is a nice way to run it in batch as well.
http://www.mol.biol.ethz.ch/wuthrich/software/molmol

Jurgen

    Drs Jurgen F. Doreleijers
    NMR spectroscopy, Utrecht University,  The Netherlands
    mailto:[email-masked]
    http://www-nmr.chem.uu.nl/~jurgen

----------

make a search in the web for a programm Profit, it is a powerfull unix
programm that allow you to make a protein superimposition also in batch
mode.
Maybe you can find it at http://www.biochem.ucl.ac.uk/~martin/swreg.html
||  Dr. Rino Ragno                      E-mail: [email-masked]       ||
||  Institute for Biomedical Computing      or: [email-masked]      ||
||  Center for Molecular Design             or: [email-masked]  ||
||  Box8036, Washington University      Phone : 314-362-2272            ||
||  700 South Euclid Avenue             FAX   : 314-362-0234            ||
||  St. Louis, Missouri 63110                                           ||

----------

Have a look at the Molecular Modelling toolkit at:
  http://starship.skyport.net/crew/hinsen/mmtk.html
It contains the necessary superposition code, and making a batch mode
program that uses it is a simple matter (maybe 10 lines of code).
I could even write you that small piece of code, if I knew
what exactly you want the program to do with the superposed
structure!
Konrad Hinsen                            | E-Mail: [email-masked]
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais

--------------

  You might look into a program called MOE, by the Chemical Computing
Group.  It has very nice 3D homology modeling capabilities and will run in
batch mode.
                    Abby Parrill, Ph.D.

Currently:         Chemistry Department
                 Michigan State University
                East Lansing, MI  48824-1322
                 [email-masked]
Soon:               Chemistry Department
                   University of Memphis
                    Memphis, TN  38152
Computational Research on Materials Institute at University of Memphis
                         (CROMIUM)

----------

I'd highly recommend VMD. It's available for many platforms (SGI, Linux,
AIX, HPUX), it's free and very flexible due to a (TCL-like?) scripting
language. Check http://www.ks.uiuc.edu/Research/vmd/ for more.

Dr. Christoph Steinbeck (mailto:[email-masked] -
http://seneca.ice.mpg.de/~stein)
Max-Planck-Institute of Chemical Ecology (http://www.ice.mpg.de)
Tatzendpromenade 1a, 07745 Jena, Germany
Soaring Bear Ph.D. Research Pharmacologist, Informatics,
Chemistry & Biochemistry, Herbalist & Healthy Lifestyles
Herbal Science:  http://www.amfoundation.org/herbmed.htm
My web tools:      http://www.dakotacom.net/~bear
email: [email-masked],  [email-masked]
fax: 559-663-5833, 520-795-9350

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---------------------REPLY 10------------------------------------------

Hi again,

think you misunderstood me, I already have the postscript-code (we do
not have this journal here), so I got i sent from somewhere else. 

lookin forward to your summary...

bye,
cr

Christian Rummey, Dipl. Chem.
Institut fuer Organische Chemie, Universitaet Wuerzburg
mailto:[email-masked]
registered linux user #92917

I suggest you try TINKER from Dr. Ponder's group.

Dave

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THANK YOU ALL, MERRY CHRISTMASS AND HAPPY Y2K!

Cherif
.......................................................................
 Cherif F. Matta		  	tel. (905) 525-9140 ext. 22502
 Chemistry Department                   fax  (905) 522-2509
 McMaster University                      
 Hamilton, Ontario, CANADA L8S 4M1.
.......................................................................