[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: modeller



Hi Hailong,

I include a recent  message about the inadequacy of modeller scores when
comparing models generated with different sets of restraints.

If you want to evaluate your model you can use a wide variety  of external
programs: 
http://salilab.org/modeller/methenz/

best
Andras




Andras Fiser wrote:
> 
> Hi Asim,
> 
> The  energy scores in modeller are not comparable if you use different sets of
> restraints i.e. including/excluing disulfide restrainst in your case.
> 
> Scores only from the same run i.e. by generating several models, can be
> compared.
> 
> otherwise the overall energy score is included in the header of the coordinate
> file as "REMARK MODELLER OBJECTIVE FUNCTION:  "
> 
> Best,
> 
> Andras
> 
> please take advantage (so others can benefit too) of our modeller user list if
> you have other questions.
> http://salilab.org/cgi-bin/lwgate/lwgate/MODELLER_USAGE/
> 
> Asim Kumar Debnath wrote:
> >
> >  Hi Andras:
> >     I have modeled a protein using your program Modeler. The target
> > sequence has two cystine residues which may form a disulfide bond but
> > there is no experimental evidence on that. I have modeled both without a
> > disulfide bond and with a disulfide bond (by using special_patches
> > subroutine). Now I want to compare which one is the energetically best
> > probable structure between these two.
> >     I would greatly appreciate if you could give some advise how to
> > proceed in Modeler to find out which one is the most likely model. How
> > do I get the overall energy of the 3D-model in your program?
> >     Thank you in advance for your help.
> >     Regards,
> >
> > Asim
> >
> > =======================================================================
> >
> >              ***
> >              ***                Asim K. Debnath, Ph.D.
> >             ****                Associate Member
> >            ****                 Lindsley F. Kimball Research Institute
> >           ****  ***             The New York Blood Center
> >          ****    ****           310 E 67 Th Street
> >         ****  **  ****          New York, NY 10021
> >        ****  ****  ****         Tel. (212) 570-3373
> >       ****    **    ****        Fax. (212) 570-3299
> >        ****************         E-mail: 
> >         **************
> >
> > ========================================================================
> 
> --
>     ,
> Andras Fiser, PhD            # phone: (212) 327 7216
> The Rockefeller University   # fax:   (212) 327 7540
> Box 270, 1230 York Avenue    # e-mail:
> New York, NY 10021-6399, USA # http://salilab.org/~andras



Hai-Long Wang wrote:
> 
> At 02:20 PM 6/22/2001 -0400, you wrote:
> Hi, Andras
> 
> My protein has several disulf bonds. I had tried modeller to built model
> protein both with patch and without patch command. When the patch command
> not include, the disuf bonds are not there, but it has overall higher
> score. Is there any way in modeller to rebuilt the disuf bonds and keep the
> rest unchange?
> 
> Thank you.
> 
> Hailong
> ******************************************************************************
> Hai-Long Wang Ph.D.                                Tel: (507)284-5297
> Receptor Biology Laboratory                        Fax: (507)284-9420
> 1-149, Medical Science Building        email: 
> Mayo Foundation                             
> Rochester, MN 55905
> ****************************************************************************
> **

-- 
    ,
Andras Fiser, PhD            # phone: (212) 327 7216
The Rockefeller University   # fax:   (212) 327 7540 
Box 270, 1230 York Avenue    # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras