- modeller_usage - salilab.org

Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 123
by Ashish Runthala 19 Oct '11

19 Oct '11

Sir Ben is correct. But there is an option to let your model be biased to its actual native state, instead of forcing it to the topology of your templates. Select good templates which you might have already done correctly. Now if you know how to make a correct representative alignment for your target, that is the best choice. Or if you don't try to harness continuous or discontinuous reliable structural folds from templates as per your constraints. Don't rely simply on MD to relax the models. If your first model is distant from its native state, no way you can pull it through. So focus on template selection and correct alignment to build your model through these reliable scaffolds. Good Luck Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Wednesday, October 19, 2011 12:12:24 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 123 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. Re: Modeling GPCRs (Modeller Caretaker) 2. Re: Modeling GPCRs (Hugo Gutierrez de Teran) ---------------------------------------------------------------------- Message: 1 Date: Tue, 18 Oct 2011 17:52:46 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] Modeling GPCRs To: Maggie Pruitt <mamdahl(a)iastate.edu> Cc: modeller_usage(a)salilab.org Message-ID: <4E9E1F5E.8010507(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 10/18/11 1:57 PM, Maggie Pruitt wrote: > I am interested in using Modeller for predicting the structure of the G > protein-coupled receptor I study. This protein does not have any > homologous proteins in the PDB database and there is no experimental > data to help model the protein. Knowing this, can Modeller provide an > accurate structure of my protein to use in molecular dynamics > simulations? I understand that I can choose other crystallized GPCRs to > use as templates, but I am concerned that since Modeller is a homology > modeling program that the end model would simply look like my protein > forced onto the template structure. Yes, you are exactly correct. Modeller is not limited to using homologs as templates; it can use any protein that you believe is structurally similar to the protein you intend to model. But if you choose a template that is not similar, you will likely get a poor model. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Wed, 19 Oct 2011 08:42:21 +0200 From: Hugo Gutierrez de Teran <hugo.teran(a)usc.es> Subject: Re: [modeller_usage] Modeling GPCRs To: modeller_usage(a)salilab.org Message-ID: <CAG02diR1jQJizHkK4vM0RQm+VaCg0zke_QYMAT_8fPiDtJp6vg(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Maggie, We have developed GPCRModSim, a web server that facilitates the process of modeling GPCRs using Modeller as a back end modeling tool ( http://gpcr.usc.es) In particular, once you upload your sequence or swissprot code, you will get an optimized alignment with all crystallized GPCRs (you can choose also between templates in the active or inactive conformations). The server will recommend you the most suitable template based on TM homologies, although you can further inspect this and change the default selection on the basis of homologies between particular regions. Please visit http://gpcr.usc.es For a test case, the H1 histamine receptor modeled with excelent accuracy, see the tutorial at http://gpcr.usc.es/tutorial There are several other features, like the possibility of loop refinement (using loopmodel routines) and the MD simulation of your simulated model in an atomistic model of the membrane (using GROMACS routines). Hugo -- Hugo G. de Teran, PhD. "Parga Pondal" Research fellow Fundaci?n P?blica Galega de Medicina Xen?mica - SERGAS Santiago de Compostela (SPAIN) Phone +34 881813873 e-mail:hugo.teran@usc.es http://webspersoais.usc.es/hugo.teran 2011/10/18 Maggie Pruitt <mamdahl(a)iastate.edu> > Hello, > > I am interested in using Modeller for predicting the structure of the G > protein-coupled receptor I study. This protein does not have any homologous > proteins in the PDB database and there is no experimental data to help model > the protein. Knowing this, can Modeller provide an accurate structure of my > protein to use in molecular dynamics simulations? I understand that I can > choose other crystallized GPCRs to use as templates, but I am concerned that > since Modeller is a homology modeling program that the end model would > simply look like my protein forced onto the template structure.**** > > If anyone can give me some further insight on this manner, I would greatly > appreciate it. > > Thanks in advance for your help! > > Sincerely, > > Maggie > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > > -- -- Hugo G. de Teran, PhD. "Parga Pondal" Research fellow Fundaci?n P?blica Galega de Medicina Xen?mica - SERGAS Santiago de Compostela (SPAIN) Phone +34 881813873 e-mail:hugo.teran@usc.es http://webspersoais.usc.es/hugo.teran -- -- Hugo G. de Teran, PhD. "Parga Pondal" Research fellow Fundaci?n P?blica Galega de Medicina Xen?mica - SERGAS Santiago de Compostela (SPAIN) Phone +34 881813873 e-mail:hugo.teran@usc.es http://webspersoais.usc.es/hugo.teran

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Re: [modeller_usage] Modeling GPCRs
by Hugo Gutierrez de Teran 18 Oct '11

18 Oct '11

Maggie, We have developed GPCRModSim, a web server that facilitates the process of modeling GPCRs using Modeller as a back end modeling tool ( http://gpcr.usc.es) In particular, once you upload your sequence or swissprot code, you will get an optimized alignment with all crystallized GPCRs (you can choose also between templates in the active or inactive conformations). The server will recommend you the most suitable template based on TM homologies, although you can further inspect this and change the default selection on the basis of homologies between particular regions. Please visit http://gpcr.usc.es For a test case, the H1 histamine receptor modeled with excelent accuracy, see the tutorial at http://gpcr.usc.es/tutorial There are several other features, like the possibility of loop refinement (using loopmodel routines) and the MD simulation of your simulated model in an atomistic model of the membrane (using GROMACS routines). Hugo -- Hugo G. de Teran, PhD. "Parga Pondal" Research fellow Fundación Pública Galega de Medicina Xenómica - SERGAS Santiago de Compostela (SPAIN) Phone +34 881813873 e-mail:hugo.teran@usc.es http://webspersoais.usc.es/hugo.teran 2011/10/18 Maggie Pruitt <mamdahl(a)iastate.edu> > Hello, > > I am interested in using Modeller for predicting the structure of the G > protein-coupled receptor I study. This protein does not have any homologous > proteins in the PDB database and there is no experimental data to help model > the protein. Knowing this, can Modeller provide an accurate structure of my > protein to use in molecular dynamics simulations? I understand that I can > choose other crystallized GPCRs to use as templates, but I am concerned that > since Modeller is a homology modeling program that the end model would > simply look like my protein forced onto the template structure.**** > > If anyone can give me some further insight on this manner, I would greatly > appreciate it. > > Thanks in advance for your help! > > Sincerely, > > Maggie > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > > -- -- Hugo G. de Teran, PhD. "Parga Pondal" Research fellow Fundación Pública Galega de Medicina Xenómica - SERGAS Santiago de Compostela (SPAIN) Phone +34 881813873 e-mail:hugo.teran@usc.es http://webspersoais.usc.es/hugo.teran -- -- Hugo G. de Teran, PhD. "Parga Pondal" Research fellow Fundación Pública Galega de Medicina Xenómica - SERGAS Santiago de Compostela (SPAIN) Phone +34 881813873 e-mail:hugo.teran@usc.es http://webspersoais.usc.es/hugo.teran

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Modeling GPCRs
by Maggie Pruitt 18 Oct '11

18 Oct '11

Hello, I am interested in using Modeller for predicting the structure of the G protein-coupled receptor I study. This protein does not have any homologous proteins in the PDB database and there is no experimental data to help model the protein. Knowing this, can Modeller provide an accurate structure of my protein to use in molecular dynamics simulations? I understand that I can choose other crystallized GPCRs to use as templates, but I am concerned that since Modeller is a homology modeling program that the end model would simply look like my protein forced onto the template structure. If anyone can give me some further insight on this manner, I would greatly appreciate it. Thanks in advance for your help! Sincerely, Maggie

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Re: [modeller_usage] Modeller on SGE
by Modeller Caretaker 18 Oct '11

18 Oct '11

On 10/18/11 6:02 AM, Matías wrote: > HI, I´m trying to run modeller in multiple cores on a Cluster with > SGE. Do you have an example script to do this? No, since it is highly dependent on your SGE setup. And it depends what you mean by "run modeller". There are two classes in Modeller for running on SGE systems: sge_qsub_job and sge_pe_job. The first uses 'qsub' from within the Modeller run to start an SGE job to do the computation (typically you run Modeller on your head node or some other machine which can 'qsub' to your cluster). The second is designed to be used in a Modeller job which is running on your cluster in a PE; it will allow Modeller to use all the nodes in that PE. A basic usage of the first for comparative modeling would be something like (see also examples/automodel/model-parallel.py): from modeller import * from modeller.automodel import * from modeller.parallel import * j = sge_qsub_job(maxslave=10) env = environ() a = automodel(env, alnfile=...) a.starting_model = 1 a.ending_model = 100 a.use_parallel_job(j) a.make() This will automatically 'qsub' an SGE array job containing 10 tasks when you call a.make(), so that the modeling is split between 10 processors. See also http://salilab.org/modeller/9.10/manual/node438.html Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Request for papers.
by Sehrish Batool 18 Oct '11

18 Oct '11

Sir I request you to send me full length papers of the following, 1. N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali. Comparative Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006. 2. M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000. 3. A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993. 4. A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures, Protein Science 9. 1753-1773, 2000 Thank you

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Re: [modeller_usage] Restraining Secondary Structure
by bharat lal 17 Oct '11

17 Oct '11

Hi, I am modelling a sequence in which I am restraining some portions of the sequence to be helix as I have copied that sequence from a known structure. But I want to ask whether the same restrained sequence would also be same in real or not. What is the basis of restraining the structure to be helix or sheets ?? --------- Bharat

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Changing the directory.
by Sehrish Batool 17 Oct '11

17 Oct '11

I am using Modeller9.10 and I am unable to define directry in Command Prompt using 'Dir' keyword. Please tell me how can I define it and where Did I made mistake. The command that I used is : Dir = C:\Program Files\Modeller9.10\examples\automodel

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Correct the small scripting error
by Ashish Runthala 17 Oct '11

17 Oct '11

Dear MODELLERS, I tried writing a script to automatically take 3 templates from the current folder and do iterative modeling for the same target sequence. i.e., I want to run Modeller with three templates (2 fixed (1SHWA, 1SHXA) + 1 variable, taken as different individual template files from the current folder iteratively). def align(fileName): #fileName iteratively contains name of all pdb files log.verbose() env = environ() env.io.atom_files_directory = ['.', '../atom_files'] pdbfile=fileName + 'A' aln = alignment(env) for (code,code,atomfile, chain) in (('1SHWA','1SHXA','1SHX','A'),(pdbfile,pdbfile,fileName,'A')): mdl = model(env, file=atomfile, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(mdl, atom_files=atomfile, align_codes=code) There is some mistake in last four lines as only two templates are coming in the alignment file and not the third one. So correct my mistake in this piece of code. Thanks, Ashish -- Ashish Runthala, Lecturer, Structural Biology Cell, Cabin: 3222-U Biological Sciences Group, Faculty Division III, Birla Institute of Technology & Science, Pilani Rajasthan, INDIA - 333 031 Website: https://sites.google.com/site/ashishrunthala/ Phone: +91-1596-245073-273 (O) +91-7597971146 (M) Fax: +91-1596-244183 E-mail: ashishr(a)bits-pilani.ac.in ashish.runthala(a)gmail.com

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energy
by Jin-Rui Xu 16 Oct '11

16 Oct '11

Hi there, What is the indication of modeller mod energy? The higher the better? Thanks!

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Regarding align2d & CS-BLAST alignments PLEASE ANSWER ME QUICKER ..I AM STUCK UP IN A FEW CASES
by Ashish Runthala 03 Oct '11

03 Oct '11

Dear Modellers and Sir Ben Webb, I am finding a critical difference in the pairwise alignment computed by MODELLER and the corresponding alignment cognitive to the CS-BLAST undertaken alignment. These are the differences. Will someone help me understanding why there is the case of shifted alignments in the the alignment case mentioned below for the following alignments of templates 2Q7BA and 3PP9A for the CASP8 target T0400? I have written TARGE in the MODELLER Alignment file for target sequence for better one-to-one alignment residue correlation. On top of it the CS-BLAST residue order is not available in the template PDB files. So i am confused..Where CS-BLAST has got the altered sequences from, when i precisely called the PDB for it. 2Q7BA ALIGNMENT MODELLER ALIGNMENT 2Q7BA>FQGMEIKEYENNPYHLAQLVDLINYCQNIEAKLDIKMAEQDDIFQIENYYQNRKGQFWIALEN-EKVVGSIALLRIDDKTAVLKKFFTYPKYRGNPVRLGRKLFERFMLFARASKFTRIVLDTPEKEKRSHFFYENQGFKQITRDELDVDYIFPDRDSRIYVKLL--* TARGE>M-AINIIEY-NRSY-KEELIEFILSIQKNEFNIKIDRDDQPDLENIEHNYLNSGGQFWLAINNHQNIVGTIGLIRLDNNMSALKKMFVDKGYR-N-LKIGKKLLDKVIMTCKEQNIDGIYLGTIDKFISAQYFYSNNGFREIKRGDLPSSFPKLDVDNRFYYRNLKD* CS-BLAST ALIGNMENT Query: 1 MAINIIEYNRSYKEELIEFILSIQKNEFNIKIDRDDQPDLENIEHNYLNSGGQFWLAINN 60 M I E N + +L++ I Q E + I +Q D+ IE+ Y N GQFW Sbjct: 20 MEIKEYENNPYHLAQLVDLINYCQNIEAKLDIKMAEQDDIFQIENYYQNRKGQFW-IALE 78 Query: 61 HQNIVGTIGLIRLDNNMSALKKMFVDKGYRN--LKIGKKLLDKVIMTCKEQNIDGIYLGT 118 ++ +VG+I L+R+D+ + LKK F YR +++G+KL ++ ++ + I L T Sbjct: 79 NEKVVGSIALLRIDDKTAVLKKFFTYPKYRGNPVRLGRKLFERFMLFARASKFTRIVLDT 138 Query: 119 IDKFISAQYFYSNNGFREIKRGDLPSSFPKLDVDNRFYYRNLK 161 +K + +FY N GF++I R +L + D D+R Y + L Sbjct: 139 PEKEKRSHFFYENQGFKQITRDELDVDYIFPDRDSRIYVKLLD 181 3PP9A ALIGNMENT MODELLER ALIGNMENT 3PP9A>SLLIRELETNDLDNFPEIDDSFIVNARLMLSLSKVNRRIEYTVEDVPSYEKSYLELVYNEYINKPNQIIYIALLHNQIIGFIVLKKNWNNYAYIEDITVDKKYRTLGVGKRLIAQAKQWAKEGNMPGIMLETQNNNVAACKFYEKCGFVIGGFDFLVYKGLNMTSDEVAIYWYLHF* TARGE>------M---AI-NIIEYNRSY-KEELIEFILS-I-QKNEFNIK-IDRDDQPDLENIEHNYLNSGGQFWLAINNHQNIVGTIGLIRLDNNMSALKKMFVDKGYRNLKIGKKLLDKVIMTCKEQNIDGIYLGTIDKFISAQYFYSNNGFREIKRGDLPSSFPKLDVDNRFYYRNLKD* CS-BLAST ALIGNMENT Query: 1 MAINIIEYNRSYKEELIE----------FILSIQKNEFNIKIDRDDQPDLEN-------- 42 M++ I E + + E +LS+ K I+ +D P E Sbjct: 4 MSLLIRELETNDLDNFPEIDDSFIVNARLMLSLSKVNRRIEYTVEDVPSYEKSYLQNDNE 63 Query: 43 --IEHNYLNSGGQFWLAINNHQNIVGTIGLIRLDNNMSALKKMFVDKGYRNLKIGKKLLD 100 + + Y+N Q H I+G I L + NN + ++ + VDK YR L +GK+L+ Sbjct: 64 ELVYNEYINKPNQIIYIALLHNQIIGFIVLKKNWNNYAYIEDITVDKKYRTLGVGKRLIA 123 Query: 101 KVIMTCKEQNIDGIYLGTIDKFISAQYFYSNNGFRE 136 + KE N+ GI L T + ++A FY GF Sbjct: 124 QAKQWAKEGNMPGIMLETQNNNVAACKFYEKCGFVI 159 Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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