- modeller_usage - salilab.org

[Fwd: modeling crosslinked homodimeric protein]
by Modeller Caretaker 26 Mar '07

26 Mar '07

-------- Original Message -------- Subject: modeling crosslinked homodimeric protein Date: Mon, 26 Mar 2007 10:29:24 +0530 From: Archana Chavan <archananiper(a)gmail.com> To: modeller-care(a)salilab.org hello everybody, i am tryong to model the structure of enzyme which is crosslinked homodimeric protein two identical chains of protein are crosslinked in opposite orientation to form the two compete active sites. that is, both chains contribute fo the foramtion of aech of the active site. (there are 64 hydrogen bonds involved in inetaction between two chains) i tried to model to chains seperatly and superimpossed bsed on template, but the orientation of the chains is not giving the proper active site, so how i can model the whole protein, i.e. both the chains simultaneously so that i can get full active site? or is there any way by which seperatly modeled chaines can be put together? please suggest any solution for this problem. Thanks in advance. -- Archana Chavan MS (Pharm)Pharmacoinformatics National Institute of Pharmaceutical Education and Research (NIPER) Mohali-160 062 Punjab, India. phone:+91-(0)-9888847223 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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alignment of multiple templates
by Bo Yang 26 Mar '07

26 Mar '07

Hello, Modeller: I try to do a multiple structural alignment using the example of "salign.py" script. The command went through, but the alignment file only contained the last template sequence. I have attached my script and the alignment files generated. My pdb files containe only single chain. I can't figure out what could be wrong with my script. Why it always return the last template sequece. I use modeller 8v1. Thank you very much for your help! Bo --------------------------------- Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. log.verbose() env = environ() env.io.atom_files_directory = "./:../atom_files/" aln = alignment(env) for (code) in (('2HI4-1A2'), ('1PQ2-2C8A'), ('1OG5-2C9A')): mdl = model(env, file=code, model_segment=('FIRST:@', 'END:')) aln.append_model(mdl, atom_files=code, align_codes=code) for (weights, write_fit, whole) in (((1., 0., 0., 0., 1., 0.), False, True), ((1., 0.5, 1., 1., 1., 0.), False, True), ((1., 1., 1., 1., 1., 0.), True, False)): aln.salign(rms_cutoffs=(3.5, 6., 60, 60, 15, 60, 60, 60, 60, 60, 60), normalize_pp_scores=False, rr_file='$(LIB)/as1.sim.mat', overhang=30, gap_penalties_1d=(-450, -50), gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0, dendrogram_file='1is3A.tree', alignment_type='tree', # If 'progresive', the tree is not # computed and all structues will be # aligned sequentially to the first #ext_tree=True, # Tree building can be avoided if the tree # is input #input_weights_file='1is3A_exmat.mtx', feature_weights=weights, # For a multiple sequence alignment only # the first feature needs to be non-zero improve_alignment=True, fit=True, write_fit=write_fit, write_whole_pdb=whole, output='ALIGNMENT QUALITY') aln.write(file='test1a.pap', alignment_format='PAP') aln.write(file='test1a.ali', alignment_format='PIR') aln.salign(rms_cutoffs=(1.0, 6., 60, 60, 15, 60, 60, 60, 60, 60, 60), normalize_pp_scores=False, rr_file='$(LIB)/as1.sim.mat', overhang=30, gap_penalties_1d=(-450, -50), gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0, dendrogram_file='1is3A.tree', alignment_type='progressive', feature_weights=[0]*6, improve_alignment=False, fit=False, write_fit=True, write_whole_pdb=False, output='QUALITY') >P1;1OG5-2C9A structureX:1OG5-2C9A: 30 :A: 490 :A:undefined:undefined:-1.00:-1.00 PPGPTPLPVIGNILQIGIKDISKSLTNLSKVYGPVFTLYFGLKPIVVLHGYEAVKEALIDLGEEFSGRGIFPLAE RANRGFGIVFSNGKKWKEIRRFSLMTLRNFGMGKRSIEDRVQEEARCLVEELRKTKASPCDPTFILGCAPCNVIC SIIFHKRFDYKDQQFLNLMEKLNENIEILSSPWIQVYNNFPALLDYFPGTHNKLLKNVAFMKSYILEKVKEHQES MDMNNPQDFIDCFLMKMEKEKHNQPSEFTIESLENTAVDLFGAGTETTSTTLRYALLLLLKHPEVTAKVQEEIER VIGRNRSPCMQDRSHMPYTDAVVHEVQRYIDLLPTSLPHAVTCDIKFRNYLIPKGTTILISLTSVLHDNKEFPNP EMFDPHHFLDEGGNFKKSKYFMPFSAGKRICVGEALAGMELFLFLTSILQNFNLKSLVDPKNLDTTPVVNGFASV PPFYQLCFIPV* _aln.pos 10 20 30 40 50 60 1OG5-2C9A PPGPTPLPVIGNILQIGIKDISKSLTNLSKVYGPVFTLYFGLKPIVVLHGYEAVKEALIDLGEEFSG _consrvd _aln.pos 70 80 90 100 110 120 130 1OG5-2C9A RGIFPLAERANRGFGIVFSNGKKWKEIRRFSLMTLRNFGMGKRSIEDRVQEEARCLVEELRKTKASP _consrvd _aln.pos 140 150 160 170 180 190 200 1OG5-2C9A CDPTFILGCAPCNVICSIIFHKRFDYKDQQFLNLMEKLNENIEILSSPWIQVYNNFPALLDYFPGTH _consrvd _aln.pos 210 220 230 240 250 260 1OG5-2C9A NKLLKNVAFMKSYILEKVKEHQESMDMNNPQDFIDCFLMKMEKEKHNQPSEFTIESLENTAVDLFGA _consrvd _aln.po 270 280 290 300 310 320 330 1OG5-2C9A GTETTSTTLRYALLLLLKHPEVTAKVQEEIERVIGRNRSPCMQDRSHMPYTDAVVHEVQRYIDLLPT _consrvd _aln.pos 340 350 360 370 380 390 400 1OG5-2C9A SLPHAVTCDIKFRNYLIPKGTTILISLTSVLHDNKEFPNPEMFDPHHFLDEGGNFKKSKYFMPFSAG _consrvd _aln.pos 410 420 430 440 450 460 1OG5-2C9A KRICVGEALAGMELFLFLTSILQNFNLKSLVDPKNLDTTPVVNGFASVPPFYQLCFIPV _consrvd

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changes in MODELLER9 optimization & DNA denaturation
by RYAN PAVLOVICZ 22 Mar '07

22 Mar '07

Hi. I just upgraded from MODELLER8v2 to 9v1 and am experiencing problems when modelling a protein-DNA complex in that the DNA is denaturing after optimization. When I use the same modelling script in 8v2, the DNA stays in its double-helical form, even when i use md_level= refine.very_slow. Can anyone explain to me what changes in the optimizers were made that cause this denaturation? I am using the MODELLER residue types ADE, GUA, CYT, and THY for the modelling. Thanks! ryan

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secondary structure assignment and patching
by Ryan 22 Mar '07

22 Mar '07

The template for one of my models has a large region in the middle of its sequence that shares no homology to my target sequence. Fortunately this region does not interact with the catalytic region in which I am interested, so I am able to remove this segment from the model. This means than my final model is composed of two chains. The problem I am having is with the secondary structure assignment to the second chain of the model. Without any explicit special secondary structure assignment the first chain of my model faithfully replicates the secondary structures of the template, while the second chain is lacking most if not all secondary structure. I know I could fix this problem by adding special restraints, but would rather have the model pick up secondary structure from the template. I am doing this modelling with default patching off. After a lot of testing, it seems that the N and C terminal patches are the cause of this loss in secondary structure to only the second chain of my model. If I comment out the patches to the protein termini but keep the patches I'm making to the DNA in my model, then I get the results I am looking for. Anyone have an idea why this is happening? Here is my input file: from modeller import * from modeller.automodel import * log.verbose() env = environ() env.patch_default = False env.io.hydrogen = env.io.hetatm = True env.io.atom_files_directory = './:~/homology' class mymodel(automodel): def special_patches(self, aln): self.patch(residue_type='5MC2', residues=(self.residues['253:C'])) self.patch(residue_type='DEO1', residues=(self.residues['248:C'])) ... self.patch(residue_type='5PHO', residues=(self.residues['248:C'])) self.patch(residue_type='5PHO', residues=(self.residues['260:D'])) # adjust 3' hydroxyl terminals of DNA strands self.patch(residue_type='3TER', residues=(self.residues['259:C'])) self.patch(residue_type='3TER', residues=(self.residues['271:D'])) # manually patch N termini self.patch(residue_type='NTER', residues=(self.residues['1:A'])) self.patch(residue_type='ACE ', residues=(self.residues['166:B'])) # manually patch C termini self.patch(residue_type='CTER', residues=(self.residues['165:A'])) self.patch(residue_type='CTER', residues=(self.residues['247:B'])) a = mymodel(env, alnfile = 'alignment.ali', knowns = ('template1','template2'), sequence = 'model3') a.starting_model= 1 a.ending_model = 1 a.make() I'd appreciate any help. Thanks! ryan

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HYP and alignment from other than modeller
by yuemin liu 21 Mar '07

21 Mar '07

Hi everyone, Is that possible to model HYP(Hydroxylproline) containing protein with PRO? I found HYP in the modeller lib, but no one-letter code for HYP. Another question is that how feasible is we use alignment from other program like blast when do modeling. Thanks, Liu, Yuemin ____________________________________________________________________________________ Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. http://games.yahoo.com/games/front

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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 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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