March 2007 - modeller_usage

how to select the best template?
by deepti 19 Mar '07

19 Mar '07

Dear modeller caretakers, please explain me the output of compare.py file,how to select the best template and what is Weighted pair-group average clustering based distance method? thanks and regards. --------------------------------------------------------------- Sequence identity comparison (ID_TABLE): Diagonal ... number of residues; Upper triangle ... number of identical residues; Lower triangle ... % sequence identity, id/min(length). 1uluA @11jw7A @12fhsA @1 1uluA @1 246 106 101 1jw7A @1 43 274 108 2fhsA @1 41 42 258 Weighted pair-group average clustering based on a distance matrix: .--- 1uluA @1.0 57.0000 | .---------------------------------------------------------- 1jw7A @1.0 58.5000 | .------------------------------------------------------------ 2fhsA @1.0 +----+----+----+----+----+----+----+----+----+----+----+----+ 58.5600 58.2900 58.0200 57.7500 57.4800 57.2100 56.9400 58.4250 58.1550 57.8850 57.6150 57.3450 57.0750

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How to incorporate NAD and water in my model
by deepti 16 Mar '07

16 Mar '07

Dear Modeller caretakers, I am trying to construct a model for a protein having a known structure for the purpose of learning Modeller. The pdb structureis in form of protein-NAD adduct. My aim is to build a similar model. Using the templates I have built a model, please tell me how to incorporate NAD and water in my model. I have read the manual 'faq' , but am confused how to change my alignment (including '.' for BLK residues and 'w' ). How do I change the template pdb files for this? How do I make my own restraint file? My alignment file is(generated by align2d.py):- >P1;1qsgA structureX:1QSG.pdb: 2 :A: 259 :A:undefined:undefined:-1.00:-1.00 GFLS-GKRILVTGVASKLSIAYGIAQAMHREGAELAFTYQND--KLKGRVEEFAAQLGSDIVLQCDVAEDASIDT MFAELGKVWPKFDGFVHSIGFAPGDQLDGDYVNAVTREGFKIAHDISSYSFVAMAKACRSMLNPGSALLTLSYLG AERAIPNYNVMGLAKASLEANVRYMANAMGPEGVRVNAISAGPIRTLAASGIK--------DFRKMLAHCEAVTP IRRTVTIEDVGNSAAFLCSDLSAGISGEVVHVDGGFSIAAMNEL* >P1;1eny sequence:1eny: : : : ::: 0.00: 0.00 AGLLDGKRILVSGIITDSSIAFHIARVAQEQGAQLVLTGFDRLRLIQRITDRLPAKAPLLELDVQNEEHLASLAG RVTEAIGAGNKLDGVVHSIGFMPQTGMGINPFFDAPYADVSKGIHISAYSYASMAKALLPIMNPGGSIVGMDFDP S-RAMPAYNWMTVAKSALESVNRFVAREAGKYGVRSNLVAAGPIRTLAMSAIVGGALGEEAGAQIQLLEEGWDQR APIGWNMKDATPVAKTVCALLSDWLPATTGDIIYADGGAHTQLL* I got a lesser objective function while using the alignment generated by clustalw. Which would be a better option? Also please suggest me ways to further refine my model so as to make it almost like the pdb structure. Thanks and Regards, Deepti

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Re: [modeller_usage] How can modeller build the structure of antibodies ?
by Modeller Caretaker 12 Mar '07

12 Mar '07

jitrayut jitonnom wrote: > I want to know that can modeller build some kind of antibodies structure > in which they have two chains (Vl and Vh). Actually, I have searched for > some similar problems but I am still in doubt. Besides, I also found the > literatures that use the modeller program to build the antibody model. > Most of them did not tell more details on how they performed to obtain > the antibody model. All I know from those papers are that there are two > ways to performs: first, model two chains from a single template; > second, model those two chains separately. Therefore, I was wondering > that which one is the best method and how to do modeling by using > modeller. Especially, after modeling the two chains (in case of the > second method) how can I concatenate these chains? See http://salilab.org/modeller/9v1/manual/node27.html For the second method, you will need to add additional constraints or do some additional modeling or docking simulations with the generated models, since Modeller will not know the relative orientation of the two chains. 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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query
by deepti 09 Mar '07

09 Mar '07

Hi, i wish to model a protein having known pdb structure. After getting a model from modeller and evaluating it I found the Dope scores from template_evaluation.py (-279092.718750)and from model_evaluation.py (-26497.847656). How do I refine the model further so that it becomes comparable with the known pdb structure? Why do I get a violatins file,Does this mean that my model is incorrect? The pdb structure is in form of the protein-NAD adduct, how do I insert NAD in my model. Can I separately model the active site and incorporate a ligand(not biological)in my model? Thanks and regards, Deepti

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Re: [modeller_usage] Errors during generate alignment file for two chains
by Modeller Caretaker 09 Mar '07

09 Mar '07

jitrayut jitonnom wrote: > and the PIR file of scfv is > >P1;scfv > sequence:scfv:1:L:123:H:::0.00: 0.00 > vmtqtpalmaaspgekvtitcsvsssisssnlhwyqqksetspkpwiygtsnlasgvpvrfsgsgsgtsysltis > smeaedaatyycqqwsnypltfgagtklelkssggggsggggggssrssl/evkllesggglvkpggslklscaas > gftfssyamswvrqtpekrlewvatissggtytyypdsvkgrftisrdnakntlylqmsslrsedtamyycarfr > ngaywgqgtlvtvsaatttapsv* > > After i run the script above i found some errros like this; > > read_al_373E> Protein specified in ALIGN_CODES(i) was not found > in the alignment file; ALIGN_CODES( 2) = scfv > > So, if anyone can help me for this problem i will be appreciated. You have two problems: 1. Alignment files are case-sensitive. The 20 standard amino acids are all in upper case, not lower case. 2. Save your alignment file in plain text. While the file here looks OK, the attachment you sent separately is formatted as Rich Text Format. If you make the file in a text editor in Windows, make sure when you save the file, you select "plain text" format. 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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Creating a dimer using model generated by modeller
by Charlie Allerston 08 Mar '07

08 Mar '07

I have created a model using a template from a dimer. I was wondering if I could incorporate this model back into the dimer in any way as I am interested in the monofacial contact between the 2 molecules? cheers charlie _________________________________________________________________ Match.com - Click Here To Find Singles In Your Area Today! http://match.engb.msn.com/

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modelling a protein-receptor complex
by Eva Vanamee 07 Mar '07

07 Mar '07

Hi, I have a protein-receptor complex (P1:R1) with known structure. I'd like to model the same receptor with another protein in complex (P2:R1). I can easily model P2 based on P1 but I am not sure how to do it in the complex. I also have a receptor, R2 that shows homology to R1 and would like to model the P2:R2 complex. I can model R2 but again I have problems modeling the complex. I am new to Modeller and would appreciate specific help with the input files. Thanks a lot in advance! - Eva

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help with modelling protein-DNA complex
by Elliott Stollar 05 Mar '07

05 Mar '07

Hi, I have looked at the manual and previous queries posted on this reoccuring subject but am unable to get modeller to model a protein-DNA complex where I treat the DNA as a rigid body. All I get back are models of the protein with no DNA present. I have done 3 things 1. Changed my pdb file so the DNA entry has HETATM and BLK (a sample below) : HETATM 1043 O5* BLK C 100 31.258 -2.296 76.212 1.00 81.62 DNA1 O HETATM 1044 C5* BLK C 100 29.867 -2.121 76.367 1.00 69.89 DNA1 C 2. Included in my alignment file a '.' for each BLK residue and a '/' to signifiy the end of a chain >P1;9ANT structureX:9ANT:FIRST :@ END : : :dros:undefined: 2.4: 0.23 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK/ .............../ ...............* >P1;1AAA sequence:1AAA:FIRST :@ END : : :human:undefined: 0.00: 0.00 RTAYTNTQLLELEKEFHFNKYLCRPRRVEIAALLDLTERKVKVWFQNRRMKHKRQTQ* 3. In my top file (running 8v2) include several varieties to turn het atoms on e.g env.io.hetatom= True SET HETATM_IO ON io_data.hetatm = True The script looks like this: INCLUDE # Include the predefined TOP routines SET ALNFILE = 'model.ali' # alignment filename SET KNOWNS = '9ANT' # codes of the templates SET SEQUENCE = '1AAA' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET HETATM_IO on SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 500 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling Any help or suggestions on something I have missed would be greatly appreciated! Elliott

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modelling of sequence without structural template.
by Archana Chavan 03 Mar '07

03 Mar '07

hello, can anybody suggest me anything about my problem? i am trying to model the structure of an oxidoreductase enzyme, for which thetemplate is of lenth shorter than the query sequence. last 47 amino acid residues at c-terminus of the protein didnot match wiht any template structure, and there are chances of these residues to be involved in formation of active site. so is there any method by which i can model this lenght of residues without alignment with any 3d structure? -- Archana Chavan MS (Pharm)Pharmacoinformatics National Institute of Pharmaceutical Education and Research (NIPER) Mohali-160 062 Punjab, India. phone:+91-(0)-9888847223

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