- modeller_usage - salilab.org

Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 35
by Ashish Runthala 29 Mar '12

29 Mar '12

Dear Sumedha, You are being confused with the assessment results, but they are correct. As you have stated, you modelled protein with, without DNA(using as a ligand) and got the RMSD difference between the models as 0.5A' in RMSd, when screened against the selected template. But this is obvious. The model with 0.1RMSD has probably better localized topology spanned over the 9bases of DNA. Check out the TM-Score of the two models against the template. As you have not provided further details about the protein length, the two models, and the template, it is difficult to precisely conclude something. TM-Score will answer your query the best. 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, March 28, 2012 4:02:12 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 11, Issue 35 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. mutate_selection.py (ARVIND PAL) 2. Re: mutate_selection.py (Modeller Caretaker) 3. Re: Regarding protein 3D structure modeling (Modeller Caretaker) 4. DNA-protein complex modelling discrepancy!! (Sumedha Roy) ---------------------------------------------------------------------- Message: 1 Date: Mon, 26 Mar 2012 12:49:18 +0530 From: ARVIND PAL <arvind.sbt(a)gmail.com> To: modeller_usage(a)salilab.org Subject: [modeller_usage] mutate_selection.py Message-ID: <CAMw18pPwUrHq13ZNb5Pu_fqe6ms4Nmg6z9cH7igxmM99w6E+TA(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear sir when i am running the *mutate_selection.py<http://salilab.org/modeller/9.9/examples/commands/mutate_selection.py> command i got the error selection contains no atom. what does it means. plz help me. *

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Model Clustering
by Ashish Runthala 28 Mar '12

28 Mar '12

Dear Modellers, I am facing some problem with the recently obtained results. Is there any way to improve the models through salign-iterative.py? The script calculates the percent topology of optimal superimposition. But, when implemented over a set of considered near-native decoys, it fails to further improve the topology (not even a bit of TM-Score undoubtedly and consistently) any single time. Rather, sometimes, the model accuracy was further decreased in terms of GDT-HA. However, this is expected as it would have taken the average overall model topology (as clear from the mutually slided model sequences in the alignment file when employed in model-multiple.py). Is there any way to precisely delimit the boundaries, where there is a huge difference (more than a specified threshold) in the backbone distance map, probably with salign-iterative so that the local model topology could be relaxed? Calpha distance 3.5A' is employed. Even with its alterations, expectations were not met. If this is incorrect, what is the mistake. Or, Is there any other way to cluster some good models through MODELLER? Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Re: [modeller_usage] Regarding protein 3D structure modeling
by Modeller Caretaker 26 Mar '12

26 Mar '12

On 3/26/12 1:30 AM, vishal Nemaysh wrote: > Regarding this (3D structure prediction) problem sir i will try to find > out some template for covering the whole query sequence during BLAST. > but there is no any single template or multiple template are found to > occupied this query. so sir plz suggest me some solution... Modeller is a package for comparative modeling, so if you have no template, you are out of luck. You either need to try harder to find a template (BLAST is not that sensitive - you can try other methods that use profile or HMM information, for example) or settle for only modeling the part of the sequence for which a template is available. 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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mutate_selection.py
by ARVIND PAL 26 Mar '12

26 Mar '12

Dear sir when i am running the *mutate_selection.py<http://salilab.org/modeller/9.9/examples/commands/mutate_selection.py> command i got the error selection contains no atom. what does it means. plz help me. *

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Regarding protein 3D structure modeling
by vishal Nemaysh 24 Mar '12

24 Mar '12

Hello Sir or all group members, i have an amino acid sequence and the length is (1106 amino acid). so plz tell me how can i model the complete 3D structure of this much lengthy sequence. thanking you, Your Sincerely -- Vishal Research Scholar, University of Delhi, North Campus Delhi-110007 M: 91+9650736653

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homology modelling with multiple subunits
by Zumot, Elia Nabil 22 Mar '12

22 Mar '12

Dear all, Is there a way to generate a homology model using several subunits as template? The protein I wish to model is a homotrimer. Am I wrong or is what is explained in "Building a model from multiple templates" not relevant here since I need the three subunits together in space (without steric clashes). Thank you in advance Elia Zomot Elia Zomot, PhD Computational and Systems Biology Department School of Medicine, University of Pittsburgh 3089 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213 Voice: 412 624 8699 - Fax: 412 648 3163 enz1(a)pitt.edu

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Is it possible to calculate energy for the given structure with MODELLER's C API and derivative with respect to all coordinates (x, y, z)?
by Valerio Lupperger 22 Mar '12

22 Mar '12

Hi, I use MODELLER (9.10) in a c-program like in http://salilab.org/modeller/manual/node456.html. As input I have one structure and its restraints. Is it possible to calculate energy for the given structure with MODELLER's C API and derivative with respect to all coordinates (x,y,z)? And if so, how is it possible? Thanks, Valerio

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Re: [modeller_usage] 2. loop refinement (rjayashree13-science@yahoo.co.in) from modeller_usage Digest, Vol 11, Issue 32
by Jan H. Löhr 22 Mar '12

22 Mar '12

>Message: 2 >Date: Thu, 22 Mar 2012 13:26:35 +0800 (SGT) >From: rjayashree13-science(a)yahoo.co.in >To: modeller_usage(a)salilab.org >Subject: [modeller_usage] loop refinement >Message-ID: > <1332393995.15170.YahooMailClassic(a)web193505.mail.sg3.yahoo.com> >Content-Type: text/plain; charset="utf-8" > >There is a script (loop.py) for the refinement of an existing model which requires the user to specify the residues to be optimized. > >How can one decide which residues need refinement? > > >Dr. Jayashree Ramana You will find a nice example in the modeller tutorial. Hoping you may better grasp the general idea, I am attempting to rephrase the gist: The residues that need to be refined usually have a high energy. Probably because your alignment was not optimal in this position, or because you do not have any information from the template(s) because of missing residues in the templates PDB or because of an insertion in the target sequence. So when you align your template and your modeller structure in a molecular imaging program you will probably see that some residues in your model do not have a corresponding template residue (naturally, this is obvious from sequence alignment as well). When there is no information from the template, modeller cannot do comparative modeling and therefore these residues will probably not be modeled well. These residues (along with residues that have been poorly modeled for other reasons) are easily spotted by the assessment-methods within modeller. I recommend looking at an energy profile such as the DOPE profile. Comparing the graphs of template and model, you will see residues that need optimization (residues whose DOPE-pseudoenergy is much higher for the model than for the template). Be careful though because of different residue lengths of template and target the DOPE profiles are not always strictly superimposable for corresponding residues may not have the same number (again because of insertions, missing residues, etc.). Summing up: You may already know the residues. Look at the alignment and identify regions where the template provides no information for your target. Try to identify these and possibly other problematic regions by using the assessment methods and obtain the DOPE profile. Actually, the answers you seek are in the end of tutorial 1 ("Basic Modeling") and at the beginning of tutorial 2 ("Advanced Modeling) along with code examples to assess your model at http://salilab.org/modeller/tutorial/. That should do the trick. Cheers Jan Jan H. Löhr Univ. Hamburg, Germany -----Original Message----- From: modeller_usage-bounces(a)salilab.org [mailto:modeller_usage-bounces@salilab.org] On Behalf Of modeller_usage-request(a)salilab.org Sent: Thursday, March 22, 2012 3:55 PM To: modeller_usage(a)salilab.org Subject: modeller_usage Digest, Vol 11, Issue 32 ------------------------------ Message: 2 Date: Thu, 22 Mar 2012 13:26:35 +0800 (SGT) From: rjayashree13-science(a)yahoo.co.in To: modeller_usage(a)salilab.org Subject: [modeller_usage] loop refinement Message-ID: <1332393995.15170.YahooMailClassic(a)web193505.mail.sg3.yahoo.com> Content-Type: text/plain; charset="utf-8" There is a script (loop.py) for the refinement of an existing model which requires the user to specify the residues to be optimized. How can one decide which residues need refinement? Dr. Jayashree Ramana

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calculate energy for a given structure with MODELLER's C API and derivative with respect to all coordinates (x, y, z)
by Valerio Lupperger 22 Mar '12

22 Mar '12

Hi, I use MODELLER (9.10) in a c-program like in http://salilab.org/modeller/manual/node456.html. As input I have one structure and its restraints. Is it possible to calculate energy for the given structure with MODELLER's C API and derivative with respect to all coordinates (x,y,z)? And if so, how is it possible? Thanks, Valerio

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loop refinement
by rjayashree13-science＠yahoo.co.in 21 Mar '12

21 Mar '12

There is a script (loop.py) for the refinement of an existing model which requires the user to specify the residues to be optimized. How can one decide which residues need refinement? Dr. Jayashree Ramana

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