October 2011 - modeller_usage

Different behavior about mislabeled HETATMs since 9v9
by Yingjie Lin 25 Oct '11

25 Oct '11

Hi MODELLER, I found different behavior between 9v7 and 9v9 (also 9v10)about mislabeled HETATMs. I haven't tried 9v8 so I don't know how it would behave. This problem occurs when dealing with a PDB file containing mislabeled HETATMs (some heteroatoms labeled as ATOM). When MODELLER reads in such a PDB file with model.read() and then writes in out with model.write(), 9v7 automatically corrects the labeling, however 9v9 and 9v10 do not. I wonder whether that's an intended change or a bug. - Yingjie

2 1

[salign] concerning the manual : feature 2 and structure superposition
by Benjamin SCHWARZ 24 Oct '11

24 Oct '11

Dear modellers, Reading the salign documentation (http://salilab.org/modeller/manual/node300.html) I have troubles understanding a specific paragraph concerning feature 2. The paragraph is the following : << The alignment produced within the routine that calculates W^2 does not generally correspond to the alignment calculated based on W. Therefore, the multiply superposed structures are not necessarily superposed based on the final multiple alignment produced by alignment.salign(). If you wish such a superposition, you can use alignment.malign3d() with fit = False and write_fit = True (the meaning of fit is different between alignment.salign() and alignment.malign3d()). >> And since I am kind of really lost on the interpretation, any clue is welcome. Thanks --Ben( S.)

2 3

Re: [modeller_usage] [clustering] does MODELLER provide tools to cluster structures ?
by Benjamin SCHWARZ 24 Oct '11

24 Oct '11

Hi Min-yi Shen, and thanks for sharing your experience, As a matter of facts, I was considering the possibility to use such a scheme as the one you describe (RMSD + linkage ). I didn't realize there could be a symmetry problem with the RMSD distance, but I guess guiding this computation with the multiple alignment should leverage the issue. --Ben Le 24 oct. 2011 à 19:38, Min-yi Shen a écrit : > My own workaround long time ago (2005) was > (1) generate N models > (2) filter out some bad models with objective values > (3) compute all-against-all RMSDs as a N-by-N matrix (just write a > double loop in py) > (4) Do hierarchical agglomerative clustering in R. > > The problem with (4) is that 1. the distance measure from step 3 may > or may not obey the triangular inequality, and 2. it varies with > cluster linkage methods. > > so, I finally opted to use some graph-based clustering methods like > MCL http://micans.org/mcl.

1 0

problems with randomization
by Igor Dvortsov 24 Oct '11

24 Oct '11

i've noticed something strange: let's try build serie of models in model_default.py-way, but with starting_model=1 and ending_model=10. we get 10 different models a1..a10. let's do it one more time with same script and we get another 10 models b1..b10. they are different between themself but coincide with previous serie, such as a1=b1..a10=b10. i just don't understand it. each model is calculated by automodel.single_model(), inside it method self.randomize_initial_structure(atmsel) is called. so randomization takes place. how it can be that these randomizations led to coinciding results? and the main question - how to make modeller give really random serie of models? kind regards, Igor.

2 1

Fwd: modeller_usage Digest, Vol 10, Issue 124
by Andrew Voronkov 23 Oct '11

23 Oct '11

Dear Modeller list administrators, I would like to change my subscription settings. I want to get not digest but messages as soon as they are sent. Sincerely yours, Andrey -------- Пересылаемое сообщение -------- 21.10.2011, 14:40, modeller_usage-request(a)salilab.org: 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: modeller_usage Digest, Vol 10, Issue 123 (Ashish Runthala) 2. induced fit modeling by Modeller or ModLoop (Andrew Voronkov) ---------------------------------------------------------------------- Message: 1 Date: Wed, 19 Oct 2011 16:17:34 +0530 (IST) From: Ashish Runthala <ashishr(a)bits-pilani.ac.in> Subject: Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 123 To: modeller usage <modeller_usage(a)salilab.org> Message-ID: <8607667.201091319021254484.JavaMail.root(a)mailserver.bits-pilani.ac.in> Content-Type: text/plain; charset=utf-8 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

1 0

induced fit modeling by Modeller or ModLoop
by Andrew Voronkov 21 Oct '11

21 Oct '11

Dear Modeller users, I need to model induced protein-ligand fit. Flexibility is supposed to be defined mostly by only one of the loops in the protein, so I probably don’t need to do a molecular dynamics, but can just make simulated annealing and conformational sampling for this loop. Is it possible to do it somehow in parallel with protein docking – for example with ligand present or by any other way to include ligand influence on loop position? But in general looks like the simplest way is to make loop sampling, perform docking and check final complexes by score/analyze manually. Best regards, Andrew

1 0

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

1 0

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

1 0

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

2 1

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

1 0