January 2011 - modeller_usage

Loop Modeling
by bharat lal 14 Jan '11

14 Jan '11

Hi, I have a question regarding modeling the loop of an already determined structure of a protein de novo. I want to change the entire sequence of the loop regions of the protein with random sequences and also I want to extend the length of the loops in the protein structure. I have searched through a lot of papers but I am not able to find any specific paper about such an approach.. So, I want to know can Modeller help in solving this problem and also I will be highly obliged if anybody can refer me to some good paper on De novo loop modeling .. Looking forward for a positive and fast reply,..... Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 E-mail : monu46010(a)yahoo.com

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 6
by bharat lal 13 Jan '11

13 Jan '11

Thanks for ur help But I am still not able to generate any model as after doing the alignment of the two sequences like teh way u said. Its giving the error "Sequence Difference between the alignement and pdb" . Here is my alignment file :- >P1;template structureX:template:1 :A: 230 :: : : : ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTL VTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFF-----------NYKTRAEVK FEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIED GSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGM DELYK * >P1;target sequence:target: : : : : : : : ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTL VTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFTDGYDFNDSKANYKTRAEVK FEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIED GSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGM DELYK * The error is :- Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 3567011 3483.409 3.402 read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 101) Alignment RTIFFNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNG PDB RTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADK Match ***** * * * * Alignment residue type 12 (N, ASN) does not match pdb residue type 9 (K, LYS), for align code template (atom file template), pdb residue number "101", chain "A" Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly. Another possibility is that some residues in the atom file are missing, perhaps because they could not be resolved experimentally. (Note that Modeller reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) In this case, simply replace the section of your alignment corresponding to these missing residues with gaps. read_te_288W> Protein not accepted: 1 template --------------------------------------------------- I am using model-loop.py script to generate the models. i want to know one more thing that how this script will model the structure of the loop sequence since the pdb coordinates are not present in the template file ... Regards --------- BHARAT

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MD Simulation
by asmat salim 11 Jan '11

11 Jan '11

Hi, We have constructed homology models based on templates of low sequence identity (27-28%). It was an enzyme and we also did some ligand-enzyme interaction study using Modeller. We did some superpositions of template and target structure and the deviation was below 1 Angstrom. We have submitted this to a journal and got a few comments. I need your advise in this regard. As you will notice that these are related to deducing and improving the quality of a homology model, I would be grateful if I can get a few tips in order to further improve the model quality in light of the listed parameters. A few of the points are concept based i.e. sequence identity and homology. Kindly comment on those. Here is the summary: RMSD related: The backbone could deviate from the true structure by a few angstroms and the impact of such deviation for enzyme catalysis could be huge. Therefore, the application of such models is often limited. Trying to deduce the specific interactions between the active site residues and a substrate based on such a model is thus questionable. The rmsd between the model and the template was ~1 angstrom is not the evidence of high quality of the models. The term rmsd is being mis-understood. In structure prediction, the rmsd between a homology model of the target protein and the X-ray structure of the same target protein was often calculated as the indication of the quality of the models, but not the rmsd between the model and the X-ray structure of the template. Sequence Related: The multiple alignment was only used for the phylogenetic analysis, whereas the pairwise alignments were used as a starting point to create the models. This procedure is conceptually wrong, since the alignment created by PSI-BLAST is not necessarily the best one. In fact, PSI-BLAST makes a pairwise alignment to find the most similar sequences, not to find the best alignment between the sequences. Moreover, with such a low sequence similarity (less than 30%) the best procedure to be sure of a good starting alignment is to perform a multiple alignment, and in case to use also predictions of the position of secondary structure elements, etc in order to improve as much as possible the quality of the alignment (see refs. to the CASP competitions). Then, the alignment between template(s) and model should be extrapolated by the multiple sequence alignment. Homolgy Definition: The term "homology" simply indicates the presence of a common evolutionary origin between two biological entities: therefore, two proteins are homologous or not. Somebody said that talking about "X% of homology" would be more or less the same as talking about a women who is "X% pregnant". Instead, it is correct to say that two proteins have X% of their amino acids identical. Energy Minimization: The authors do not have the energy minimized structure, which is a must for carrying out interaction analyses and if not done, leads to incorrect interpretations. They have assumed the program Modeller provides a proper energy-minimized structure with 'automodel' environment. However, published literature that use Modeller in such an environment still have been found to energy minimize the structure and only then use further. Thank you asmat

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Regarding Salign
by Ashish Runthala 11 Jan '11

11 Jan '11

Dear Modellers, Will you please tell me how salign actually functions to compute "final max quality" produced for a considered set of templates. Thanks, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Department, Faculty Division III, Birla Institute of Technology & Science - Pilani, INDIA

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Re: [modeller_usage] strategies for model refinement
by Mensur Dlakic 10 Jan '11

10 Jan '11

Thomas, I never really modeled a protein where loop conformation was crucial for the model itself, so I am usually content to refine the loops so they are stereochemically acceptable (I hope nobody reading this is cringing in horror at my relative indifference towards loop modeling). RAPPER for sure does a good job of improving Ramachandran outliers for loops up to 7-8 residues. The way it does it by "freezing" the protein outside of requested regions except for one "anchor" residue abutting the region and then samples the conformational space while making sure that rotamers with correct stereochemistry are utilized. I usually build 100 loops for each region and the program picks the one with lowest energy automatically, which is another reason I use it more than MODELLER for this purpose. For loops that are 6 or so residues, this takes less than two minutes. I would not try modeling loops that are 10+ residues, and in fact I usually omit them from my models if I have long insertions. Finally, these papers may (or may not, I haven't read them recently) offer the benchmark you were asking about: http://www.ncbi.nlm.nih.gov/pubmed/12596262 http://www.ncbi.nlm.nih.gov/pubmed/12596261 Best, Mensur At 07:14 PM 1/8/2011, Thomas Evangelidis wrote: >Mensur, are you aware of any benchmark analysis that shows RAPPER's >superiority on loop modeling over MODELLER? I am aware of one that >compares Rosetta, MODELLER and CABS on loops up to 24 aa if I remember >correctly, and shows that in short lengths all 3 programs are equivalent, >but for longer loops the combination of MODELLER with CABS prevails. > >I have several proteins with missing regions of varying length (8-47 aa) >which I want to fold. I have tried PyRosetta and MODELLER in the past but >I'm not impressed from the results of loop modeling, especially as the >length increases. I guess these routines were designed to model flexible >animo acid stretches that's why the predicted conformations adopt coiled >coils. To this end I also tried I-TASSER server (which employs Monte Carlo >with Replica Exchange for regions with no templates and is questionably >more accurate in folding long aa stretches) by supplying my initial >structure and excluding all homologues, but the meta-threading program >(LOMETS) it implements always detects traces of "homology" to some >irrelevant structures and uses them as templates. I guess my last resort >is MD with Replica Exchange but I haven't found the time yet to set up my >system and figure out a way to keep the rest of the model rigid, namely to >fold only the missing regions. > >This message is slightly off-topic, but I just wanted to share my >experience (and desperation) with other people that might find it helpful >(I hope not the desperation). > > >Thomas ========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic(a)montana.edu | ==========================================================================

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Re: [modeller_usage] model refinement
by Irene Newhouse 09 Jan '11

09 Jan '11

The discussion resulting from my question has been most interesting & most helpful! I'm saving it for future reference. The protein I'm working on almost has a missing loop - that is, someone finally managed to get crystals in which the previously missing residues were resolved. But someday, that won't be the case. I have a 2.33GHz linux box, and I started my 514-residue dimeric protein on Rosetta relax a short time after lunch on Friday. The job finished sometime Saturday night or the early hours of Sunday morning. The MolProbity score was 1.93. Thanks so much! Irene

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strategies for model refinement
by Irene Newhouse 08 Jan '11

08 Jan '11

I'm a relatively new user of modeller & successfully built a fairly nice model of a protein with 258 residues. It forms a homodimer, and has to be modeled as a dimer, because there's a very flexible loop that can easily adopt conformation that prevent dimerization if the 2nd unit isn't present. [I confirmed that by trying it]. Someone on this group suggested the Molprobity server as a way to assess model quality, for which I'm very grateful. He also suggested relaxing the structure with Rosetta, & after epic battles with python setup & my operating system, I got it up & running. Only to learn from the RosettaCommons forum that Rosetta relax doesn't scale well with chain length & isn't useful for proteins with >200 residues. I managed to get the Molprobity score down to a respectable 2.-something using lots & lots of iterations of Schrodinger Prime loop refinement & side chain minimization. It took about a week of setting up a loop, running it, checking to see if it refined, iterating 'til I could move on, etc. So I'm looking for something a bit less hands-on, if possible. Also, Schrodinger is expensive & my boss may not renew the licenses when this lot expires in March. And finally, Molprobity signaled several C-beta issues in my structure, & Schrodinger just doesn't seem to do much about those. Therefore, I'm looking for other suggestions, preferably freeware, for model refinement. I have tried some loop refinement with Modeller itself, but wasn't thrilled with the outcome. This could easily be because I couldn't find sample scripts to copy, or an explanation of how to tweak the parameters if the loop doesn't seem to be refining. If anyone can point me in those directions, I'd be grateful, too. Thanks so much!

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cyclic peptide modeling
by r.yu＠imb.uq.edu.au 05 Jan '11

05 Jan '11

Dear Users, I want to use modeller to model the cyclopeptide. Before sending question here, I checked the mail-list and found other people had asked similar questions. However, when I tried to solve my own problem based on the suggestion, I still could not get my problem resolved. I have attached the script as following: # Homology modeling by the automodel class from modeller.automodel import * # Load standard Modeller classes env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = '/home/rileiyu/model/single/atom' # Disable default NTER and CTER patching env.patch_default=False class mymodel(automodel): def special_patches(self, aln): # Link between residues 22 and 1 to make chain cyclic: self.patch(residue_type='LINK', residue_ids=('22:', '1:')) a = mymodel(env, alnfile = 'single', # alignment filename knowns = 'mii', # codes of the templates sequence = 'cmii',) # code of the target a.make() # do the actual homology modeling But when I started to model my cyclopepetide the problem appeared as: Traceback (most recent call last): File "model.py", line 21, in ? a.make() # do the actual homology modeling File "/home/rileiyu/share/modeller9v7/modlib/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/home/rileiyu/share/modeller9v7/modlib/modeller/automodel/automodel.py", line 427, in homcsr self.make_initial_model(aln) File "/home/rileiyu/share/modeller9v7/modlib/modeller/automodel/automodel.py", line 441, in make_initial_model self.generate_method(self, aln) File "/home/rileiyu/share/modeller9v7/modlib/modeller/automodel/generate.py", line 25, in transfer_xyz mdl.create_topology(aln) File "/home/rileiyu/share/modeller9v7/modlib/modeller/automodel/automodel.py", line 659, in create_topology self.special_patches(aln) File "model.py", line 13, in special_patches self.patch(residue_type='LINK', residue_ids=('22:', '1:')) TypeError: patch() got an unexpected keyword argument 'residue_ids' Can anyone here give me more suggestions please? Very appreciated for your help!

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