February 2006 - modeller_usage

as1 matrix
by Schulze, Diana 22 Feb '06

22 Feb '06

Hi. To build an alignment in MODELLER the standard is the as1 matrix. Does somebody know why this matrix is used as standard and whats the difference to pam or blosum? Thanks Dina

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Help needed concerning the alignment file
by doppelt olivia 21 Feb '06

21 Feb '06

Hello, I've been trying to use Modeller on an alignement file obtained from a clustalw use. I have the pdb file in the same repertory. I used a script, that i found in the examples files of Modeller. When I try to use Modeller, the following error is made : rdpir___648E> Alignment sequence not found in PDB file: 1 ./1tu7.pdb Here is my scipt : #! /usr/bin/env python from modeller.automodel import * import sys env = environ() ali = sys.argv[1] pdb = sys.argv[2] nb = int(sys.argv[3]) env.io.atom_files_directory = pdb a = automodel(env, alnfile=ali, knowns='1tu7', sequence='13gs') a.starting_model = 1 a.ending_model = nb a.make() Here is my alignment file 13gs-1tu7.ali: >P1;1tu7 structureX:1tu7: ::: ::: 0.00: 0.00 MS-YKLTYFSIRGLAEPIRLFLVDQDIKFIDDRIAKDDFS--SIKSQFQFGQLPCLYDGD QQIVQSGAILRHLARKYNLNGENEMETTYIDMFCEGVRDLHVKYTRMIYMAYETEKDPYI KSILPGELAKFEKLLATRGNGRNLILGDKISYADYALFEELDVHQILDPHCLDKFPLLKV FHQRMKDRPKLKEYCEKRDAAKVPVNGNGKQ* >P1;13gs sequence:13gs: : : : ::: 0.00: 0.00 MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASCLYGQLPKFQDGD LTLYQSNTILRHLGRTLGLYGKDQQEAALVDMVNDGVEDLRCKYISLIYTNYEAGKDDYV K-ALPGQLKPFETLLSQNQGGKTFIVGDQISFADYNLLDLLLIHEVLAPGCLDAFPLLSA YVGRLSARPKLKAFLASPEYVNLPINGNGKQ* the pdb file 1tu7.pdb is in the same directory. I changed a lot of things in the script or in the alignment file, it doesn't change anything. Any help would be good, Thanks in advance, Olivia Doppelt ___________________________________________________________________________ Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international. Téléchargez sur http://fr.messenger.yahoo.com

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alingment score using salign
by jo hanna 21 Feb '06

21 Feb '06

Hi If i have a set of alignments that I have generated is it possible to calculate just the score using salign in modeller? Thanks Jo

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what is the correct alignment
by rudra 21 Feb '06

21 Feb '06

hi, i'm new to homology modeling, i was trying to solve a structure by homology modeling, i want to know what is the correct alignment among these two: case 1: template abbadfaclkzcdtcfdgswchc target aabadaacckzcct----ccghc secondary structure CCCCCCCHHHHHHHHHHHHHHHH CLUSTALW * *** ** *** * ** case 2: template abbadfaclkzcdtcfdgswchc target aabadaacckzcctccghc---- secondary structure CCCCCCCHHHHHHHHHHHHHHHH CLUSTALW * *** ** *** ** regards, rudra

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Request for correcting errors
by Aparna Apurba Roy 20 Feb '06

20 Feb '06

Respected Sir/Madam, I am Miss Aparna Roy student of Rishi Biotech Institute, Thane. I am facing some problem in running the Modeller 6v2 software. Attachment ( Atm, Ali, Top files) Thanking you. Yours faithfully, Aparna Roy.

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Check_a_337E> Structure not read in
by David Mathog 15 Feb '06

15 Feb '06

First time trying to use Modeller and the log file terminates with: check_a_337E> Structure not read in. There's nothing wrong with the PDB file as far as I can tell, several other programs will read it. Modeller seems to have read the alignment alright, although this bit: (def)remove_gaps=True is a little worrisome, since there are a couple of gaps in the alignment. In fact, that's the whole point, I want to see if modeller can close the gaps so that I don't have to do it manually in a modelling program. The gaps are part of the structure that flaps around in solution so it isn't in the PDB file, but it has to be added before Gromacs will accept the structure. Thanks, David Mathog mathog(a)caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech

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How to make models from multiple sequences e.g an entire proteome
by Antony 12 Feb '06

12 Feb '06

I would like to obtain models of the entire Saccharomyces cerevisiae proteome in order to predict DNA binding proteins using structural information. How can I use modeller to quickly make a model for each protein sequence (6,702 in all)? I believe the models are already available in the Yeast SGD1 dataset but I can only view 500 models. Is there a way I can obtain all the structure files (preferrablyPDB format)? Please help Tonyngahu.

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How does Modeller handle multiple structures?
by Zoe Katsimitsoulia 10 Feb '06

10 Feb '06

Hello everyone, I am very new to modelling and working a target sequence that has just less than 27% sequence identity with another 10 proteins that have crystal structures. My target and templates are all myosin proteins, but from 2 different classes, since there are no crystal structures available for my target in its same class. I have 2 concerns/queries: 1. How will modeller handle the 10 template sequences (which themselves show a significant amount of variation at certain key positions). More specifically, a particular area of my seq alignment may read like this: template 1 xxxxxGxxxxxxxx template 2 xxxxxTxxxxxxxx template 3 xxxxxGxxxxxxxx template 4 xxxxxGxxxxxxxx template 5 xxxxxGxxxxxxxx template 6 xxxxxGxxxxxxxx template 7 xxxxxGxxxxxxxx target xxxxxTxxxxxxxx In simple terms, would modeller in this case use the coord of T in the template 2 sequence because it matches the target at that location, or will it use G because it is predominant in the majority of the structures? 2. The 10 template structures I am using are themselves in different states, for example, partially closed conformation, open, transition, inhibitor bound, etc. Is this beneficial to building my model or more detrimental? I am assuming the former based on the logic that the more info I am giving to modeller, the better my model should be. However, perhaps there is something about the way modeller works which I have not grasped that means its actually doing more harm adding the structures in different states? Thanks very much in advance, -Zoe

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Protocol of modeling a membrane protein
by Qing Zhang 08 Feb '06

08 Feb '06

Dear Modeller users: I just started using Modeller (version 8v1) and would like to find a good protocol of modeling membrane proteins that contain helices, beta-sheets, loops, and long N and C-terminal tails. By reading Modeller manual and some papers, I have a rough plan like this: 1. Find the closest sequences in PDB using Blast [done]. 2. Do sequence alignment with the best PDB structure using ClustalW [done with a score of only 15] 3. Build 10 models in Modeller with 3 repeats of very thorough VTFM optimization and MD optimization until max_molpdf <= 1E6 [done] 4. Pick the best model based on the quality of helices and beta-sheets only since loops have not been very optimized [I do not know much about verifying protein structure quality; it seems WHAT_CHECK is a good program to use; any suggestions?] 5. Optimize loops in Modeller for the above best model and obtain several loop models 6. Pick the best loop model with quality check 7. Molecular dynamics simulations? Any suggestions on this? Thanks in advance. Sincerely, Qing ====================================== Qing Zhang, Ph.D. Research Associate Department of Molecular Biology, MB-5 The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037-1000 Tel: (858) 784-2333 Fax: (858) 784-2860 Cell: (917) 509-3182 Email: qzhang(a)scripps.edu Website: www.qingzhang.info ======================================

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Add loops to a protein
by Mingfeng Yang 07 Feb '06

07 Feb '06

Dear Modeller users, I have a protein, its full sequence and most part of its structure have been known, except 4 segments of loops (6-15 residues long). Can I use modeller package to add the loops to the known core of the protein? How? Where should I begin from? I know that I definitely should delve into the tutorial or manual first, try different things and then ask question here. However I just heard this modeling package minutes ago, and just registered, downloaded, and installed it. I am in a rush to get the last step of my current project done. Hope somebody can give me some hints. Thank you very very much! Cheers, Mingfeng Yang

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