July 2009 - modeller_usage

Restraints from SAXS data
by NM Burton, Biochemistry 07 Jul '09

07 Jul '09

Hello, I'm interested in using SAXS data as restraints for model-building, so checked the modeller_usage archives... Back in January 2007 SAXS restraints were described as "still experimental, and so are probably not generally useful right now." Would this still be a fair description? Cheers, Nick ---------------------- Dr N M Burton Department of Biochemistry University of Bristol BS8 1TD, UK +44 117 3312149 nick.burton(a)bristol.ac.uk

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completing incomplete templates
by Steve Seibold 07 Jul '09

07 Jul '09

Hello Modeller I have a newbie question. I have a template structure that is incomplete. There are a couple of segment loops missing. Is it possible to use Modeller to build up the loops if I give it a complete sequence (fasta) and use the template (with missing loops)? The reason I ask is because it was suggested from another web site that Modeller could do this, but I am not convinced that it can. If not, could someone suggest a software package that could do this? Thanks for your response Steve Steve Seibold Research Asst. Professor seibold(a)chemistry.msu.edu 19B Chemistry Building Michigan State University East Lansing, MI 48824 Office 517-355-9715 ext 264

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Modeling large protein sequence having homologues with less similarity.
by Sehrish Batool 06 Jul '09

06 Jul '09

Hello, My target sequence of protein is too large containing more than 1000 amino acids and I found 4 homologues in PDB showing very less similarity i-e. two showing 28% similarity, one showing 24% and last one showing 19% similarity with my target sequence. Also the starting residues of templates have no homology with my target sequence and Modeller has to read from 1st residue of template, that bocomes impossible in this case. So now how can I model my target sequence?

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Re: [modeller_usage] modeller_usage Digest, Vol 8, Issue 45
by shilpi 06 Jul '09

06 Jul '09

thanks a lot Ben. Shilpi On Mon, Jul 6, 2009 at 9:41 AM, <modeller_usage-request(a)salilab.org> wrote: > Send modeller_usage mailing list submissions to > modeller_usage(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. regarding multiple sequence alignment (shilpi) > 2. Re: regarding multiple sequence alignment (Modeller Caretaker) > 3. Re: resuming a crashed job (Modeller Caretaker) > 4. Modeling large protein sequence having homologues with less > similarity. (Sehrish Batool) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 1 Jul 2009 14:33:12 +0200 > From: shilpi <shilpi.chaurasia(a)gmail.com> > Subject: [modeller_usage] regarding multiple sequence alignment > To: modeller_usage(a)salilab.org > Message-ID: > <eba7cb770907010533x208c0fc1j61dd26ee85ad7ed3(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > I have aligned three homologous protein sequences by > salign_profile_profile.py , but the alignment file obtained is not > accurate. > Can anyone tell me which script should I use for multiple sequence > alignment. > > thanks > Shilpi >

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resuming a crashed job
by Søren Skovstrup Hansen 02 Jul '09

02 Jul '09

hDear Modellers A very simple question: Is it possible to resume a crashed Modeller job? I was running a more or less standard automodel job, but my computer crashed after building 200 out of 250 models. Hence, is it possible to resume this job and thereby evaluating and ranking all 250 build models via e.g. the DOPE score? BW Søren S Hansen ---------------------------------------------------------------------------- ----- Søren Skovstrup Hansen, Ph.D. student, M.Sc. Biostructural Research Group, Department of Medicinal Chemistry Faculty of Pharmaceutical Sciences, University of Copenhagen DK-2100 Copenhagen, Denmark Phone office (+45) 3533 6108 Mobile (+45) 2090 9866

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regarding multiple sequence alignment
by shilpi 01 Jul '09

01 Jul '09

I have aligned three homologous protein sequences by salign_profile_profile.py , but the alignment file obtained is not accurate. Can anyone tell me which script should I use for multiple sequence alignment. thanks Shilpi

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