- modeller_usage - salilab.org

Invitation to connect on LinkedIn
by Uday Kumar 26 Apr '12

26 Apr '12

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Regarding Model Building
by Ashish Runthala 23 Apr '12

23 Apr '12

Dear Modellers, I have a pretty small question. Is there a way in MODELLER where i can completely use a single template along with its side-chain topology? So while aligned with target, I would expect that the template's backbone and side-chain relative orientations, topology and architecture is properly copied from the considered template, and then I would expect MODELLER to model the unaligned flexible chunks through the exactly copied scaffolds from the template. In normal modelling scripts, it simply harness the peptide backbone localization information from the template and then fixes the side-chains with its own algorithms. HOW CAN I GET MY QUERY SOLVED WITH AN ADDITIONAL LINE IN MODEL-SINGLE.PY TO COMPLETELY EMPLOY TEMPLATE WITH ITS PEPTIDE BACKBONE ALONG WITH SIDE-CHAINS? Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 44
by Ashish Runthala 10 Apr '12

10 Apr '12

Script is wrong, Use knowns='5fd1A' (with ChainID) because this is a protein. For ligand bound residue put a . in the alignment file, so that MODELLER can include the attached ligand too in the model. Then it will correctly call assess_methods=(assess.DOPE, assess.GA341)) (Last line of your initial set of lines). If you are using 5FD1 as the PDB file to model your sequence 1fdx, then you should definitely have the DOPE Score calculated. 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: Tuesday, April 10, 2012 11:12:30 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 11, Issue 44 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. Re: modeller_usage Digest, Vol 11, Issue 42 (Modeller Caretaker) 2. calculating DOPE score (NUTAN CHAUHAN) ---------------------------------------------------------------------- Message: 1 Date: Mon, 09 Apr 2012 20:35:37 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> To: Ashish Runthala <ashishr(a)bits-pilani.ac.in> Cc: modeller usage <modeller_usage(a)salilab.org> Subject: Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42 Message-ID: <4F83AA89.9080408(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/9/12 8:00 PM, Ashish Runthala wrote: > MODELLER based on your constructed alignment file > parsing the reliable template residues mapped against the target > ones, constructs and fixes the average alpha carbon backbone Actually all atoms that have the same name in target and template will be simply copied into the model in this case. Usually this means all backbone atoms, not just alpha carbons. > On increased sampling, > MODELLER tries best to satisfy the Lennard Jones and all the > energetic equations composing its DOPE energy function. In fact the optimization tries to minimize the molecular PDF, which includes contributions from soft sphere (not Lennard Jones). DOPE is a separate, atomistic pairwise statistical potential. It is not used in comparative modeling. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Tue, 10 Apr 2012 13:29:27 +0800 (SGT) From: NUTAN CHAUHAN <nutanbt(a)yahoo.co.in> To: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> Subject: [modeller_usage] calculating DOPE score Message-ID: <1334035767.17687.YahooMailNeo(a)web192502.mail.sg3.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" Hello all, I am trying to build a protein-ligand model using align-ligand.ali file. . Below is ?the python script to generate 5 model and to ?calculate the Dope and GA score.?but I am unable to calculate the DOPE score and GA score. Plz help from modeller import * from modeller.automodel import * log.verbose() ? ?# request verbose output env = environ() ?# create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] env = environ() a = automodel(env, alnfile='alignment.ali', ? ? ? ? ? ? ? knowns='5fd1', sequence='1fdx', ? ? ? ? ? ? ? assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 5 a.make() ? Regards, Nutan Chauhan Research Scholar Department of Biotechnology BIT, Mesra Ranchi-835215, Jharkhand ________________________________ From: "modeller_usage-request(a)salilab.org" <modeller_usage-request(a)salilab.org> To: modeller_usage(a)salilab.org Sent: Tuesday, 10 April 2012 8:58 AM Subject: modeller_usage Digest, Vol 11, Issue 43 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. Re: In what are the initial structures different? ? ? ? (Modeller Caretaker) ? 2. Re: modeller_usage Digest, Vol 11, Issue 42 (Ashish Runthala) ? 3. Re: modeller_usage Digest, Vol 11, Issue 42 (Ashish Runthala) ---------------------------------------------------------------------- Message: 1 Date: Mon, 09 Apr 2012 11:46:02 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> To: BIN ZHANG <zhngbn(a)gmail.com> Cc: modeller_usage(a)salilab.org Subject: Re: [modeller_usage] In what are the initial structures ??? different? Message-ID: <4F832E6A.5020001(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 04/08/2012 11:58 PM, BIN ZHANG wrote: > I have a question about the differences of the initial structure built > for homology modeling. Can anyone tell me how exactly are these initial > structures different? Do they differ in the secondary structures in > uncertain regions? I cannot find this information in the manual. See http://salilab.org/modeller/9.10/manual/node470.html, in particular step 3 and substep 3. The initial structures are simply randomized by calling selection.randomize_xyz(). ??? Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org? ? ? ? ? ? http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Tue, 10 Apr 2012 08:33:02 +0530 (IST) From: Ashish Runthala??? ? <ashishr(a)bits-pilani.ac.in> To: modeller usage <modeller_usage(a)salilab.org> Subject: Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42 Message-ID: ??? <15240798.16751334026982399.JavaMail.root(a)mailserver.bits-pilani.ac.in> ??? Content-Type: text/plain; charset=utf-8 Focus on the statement with ALIGN_CODES, as it is inclusive of the PDB_ID and the PDB_CHAIN used in the alignment file. So it could probably be '2AHNA' or '2AHNB'. Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ------------------------------ Message: 2 Date: Mon, 9 Apr 2012 17:21:12 +0530 From: Sumedha Roy <sumedharoy(a)gmail.com> To: modeller usage <modeller_usage(a)salilab.org> Subject: [modeller_usage] Error in ALIGN_CODES(i) Message-ID: ??? <CABFmE0dNMawUwZgsh07bsRd43+-O3Yrzq6VhfkSQJOTjp=NECA(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hello all, When I try to model my protein-DNA complex, I get the error: _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES(? ? ? 2) =? 2AHN But I see no mistake either in the alignment or the format. I've attached both the ALI file and model-ligand.py. Please help!!! -- Sumedha Roy

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calculating DOPE score
by NUTAN CHAUHAN 09 Apr '12

09 Apr '12

Hello all, I am trying to build a protein-ligand model using align-ligand.ali file. . Below is the python script to generate 5 model and to calculate the Dope and GA score. but I am unable to calculate the DOPE score and GA score. Plz help from modeller import * from modeller.automodel import * log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] env = environ() a = automodel(env, alnfile='alignment.ali', knowns='5fd1', sequence='1fdx', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 5 a.make() Regards, Nutan Chauhan Research Scholar Department of Biotechnology BIT, Mesra Ranchi-835215, Jharkhand ________________________________ From: "modeller_usage-request(a)salilab.org" <modeller_usage-request(a)salilab.org> To: modeller_usage(a)salilab.org Sent: Tuesday, 10 April 2012 8:58 AM Subject: modeller_usage Digest, Vol 11, Issue 43 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. Re: In what are the initial structures different? (Modeller Caretaker) 2. Re: modeller_usage Digest, Vol 11, Issue 42 (Ashish Runthala) 3. Re: modeller_usage Digest, Vol 11, Issue 42 (Ashish Runthala) ---------------------------------------------------------------------- Message: 1 Date: Mon, 09 Apr 2012 11:46:02 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> To: BIN ZHANG <zhngbn(a)gmail.com> Cc: modeller_usage(a)salilab.org Subject: Re: [modeller_usage] In what are the initial structures different? Message-ID: <4F832E6A.5020001(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 04/08/2012 11:58 PM, BIN ZHANG wrote: > I have a question about the differences of the initial structure built > for homology modeling. Can anyone tell me how exactly are these initial > structures different? Do they differ in the secondary structures in > uncertain regions? I cannot find this information in the manual. See http://salilab.org/modeller/9.10/manual/node470.html, in particular step 3 and substep 3. The initial structures are simply randomized by calling selection.randomize_xyz(). Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Tue, 10 Apr 2012 08:33:02 +0530 (IST) From: Ashish Runthala <ashishr(a)bits-pilani.ac.in> To: modeller usage <modeller_usage(a)salilab.org> Subject: Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42 Message-ID: <15240798.16751334026982399.JavaMail.root(a)mailserver.bits-pilani.ac.in> Content-Type: text/plain; charset=utf-8 Focus on the statement with ALIGN_CODES, as it is inclusive of the PDB_ID and the PDB_CHAIN used in the alignment file. So it could probably be '2AHNA' or '2AHNB'. Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ------------------------------ Message: 2 Date: Mon, 9 Apr 2012 17:21:12 +0530 From: Sumedha Roy <sumedharoy(a)gmail.com> To: modeller usage <modeller_usage(a)salilab.org> Subject: [modeller_usage] Error in ALIGN_CODES(i) Message-ID: <CABFmE0dNMawUwZgsh07bsRd43+-O3Yrzq6VhfkSQJOTjp=NECA(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hello all, When I try to model my protein-DNA complex, I get the error: _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = 2AHN But I see no mistake either in the alignment or the format. I've attached both the ALI file and model-ligand.py. Please help!!! -- Sumedha Roy

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Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42
by Ashish Runthala 09 Apr '12

09 Apr '12

Dear BIN ZHANG, MODELLER based on your constructed alignment file parsing the reliable template residues mapped against the target ones, constructs and fixes the average alpha carbon backbone (if you choose a single template) or an average backbone topology (for Multiple templates' local aligned chunks). Then it fits in the side chains and backbone atoms to make the model complete. However, easy saying but really a vicious circle problem, the alignment could have actually been wrong to incorrectly fit target against parsed template residues. Regardless of the earlier problems, On increased sampling, MODELLER tries best to satisfy the Lennard Jones and all the energetic equations composing its DOPE energy function. The non-physical local atomic clashes are thus minimized with every such iteration. So only you see, Restraints earlier, now with end of every such iterative step. That in fact, is the trial to leap the energetic landscape, precisely focusing on the probably erroneous regions encompassing the higher local steric clashes. The story continues until the number of iterations are over. Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA Message: 1 Date: Sun, 8 Apr 2012 23:58:13 -0700 From: BIN ZHANG <zhngbn(a)gmail.com> To: modeller_usage(a)salilab.org Subject: [modeller_usage] In what are the initial structures different? Message-ID: <602A5241-132A-4319-81BA-94C238A459AF(a)gmail.com> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Dear All: I have a question about the differences of the initial structure built for homology modeling. Can anyone tell me how exactly are these initial structures different? Do they differ in the secondary structures in uncertain regions? I cannot find this information in the manual. For example, by using a = automodel() a.starting_model = 1 a.ending_model = 50 I can built 50 different homology models starting from different initial structures, but I have want to know how these different initial structures are constructed. Thanks very much for help. Best, Bin

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Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42
by Ashish Runthala 09 Apr '12

09 Apr '12

Focus on the statement with ALIGN_CODES, as it is inclusive of the PDB_ID and the PDB_CHAIN used in the alignment file. So it could probably be '2AHNA' or '2AHNB'. Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ------------------------------ Message: 2 Date: Mon, 9 Apr 2012 17:21:12 +0530 From: Sumedha Roy <sumedharoy(a)gmail.com> To: modeller usage <modeller_usage(a)salilab.org> Subject: [modeller_usage] Error in ALIGN_CODES(i) Message-ID: <CABFmE0dNMawUwZgsh07bsRd43+-O3Yrzq6VhfkSQJOTjp=NECA(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hello all, When I try to model my protein-DNA complex, I get the error: _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = 2AHN But I see no mistake either in the alignment or the format. I've attached both the ALI file and model-ligand.py. Please help!!! -- Sumedha Roy

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In what are the initial structures different?
by BIN ZHANG 09 Apr '12

09 Apr '12

Dear All: I have a question about the differences of the initial structure built for homology modeling. Can anyone tell me how exactly are these initial structures different? Do they differ in the secondary structures in uncertain regions? I cannot find this information in the manual. For example, by using a = automodel() a.starting_model = 1 a.ending_model = 50 I can built 50 different homology models starting from different initial structures, but I have want to know how these different initial structures are constructed. Thanks very much for help. Best, Bin

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Error in ALIGN_CODES(i)
by Sumedha Roy 09 Apr '12

09 Apr '12

Hello all, When I try to model my protein-DNA complex, I get the error: _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = 2AHN But I see no mistake either in the alignment or the format. I've attached both the ALI file and model-ligand.py. Please help!!! -- Sumedha Roy

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problem with Chain.join()
by Jan Kosinski 06 Apr '12

06 Apr '12

I cannot get Chain.join() working properly for multi-chain PDB files. For example, for PDB code 2YFH, which has chains A, B, C, D, E, F,: * when I join D and E I get A, B, C, D, F as expected * but if I try to join A and B I get A, F only To reproduce run the following script: ----- from modeller import * env = environ() mdl = model(env) mdl.read(file='2yfh') print "before:" for c in mdl.chains: print c mdl.chains['A'].join(mdl.chains['B']) print "after:" for c in mdl.chains: print c mdl.write('out.pdb') print "reading new file:" mdl1 = model(env) mdl1.read('out.pdb') for c in mdl1.chains: print c ------------ will print in the log: before: <Chain 'A'> <Chain 'B'> <Chain 'C'> <Chain 'D'> <Chain 'E'> <Chain 'F'> after: <Chain 'A'> <Chain 'F'> <Chain 'F'> <Chain 'F'> <Chain 'F'> reading new file: relabel_387W> Model has multiple chains, and they do not all have a unique chain ID. Suggest you relabel them as A, B, C, etc. relabel_469W> At least one residue number in the model is duplicated. (First duplication is residue " 1", chain " A".) Suggest you renumber the residues and/or chains to avoid selecting the wrong residues (e.g. with model_segment). <Chain 'A'> <Chain 'A'> <Chain 'F'> Tested with Modeller 9v8 and Modeller 9v9. Is it a bug or expected behavior? Best regards, Jan Kosinski

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problem in modeling protein with ligand
by NUTAN CHAUHAN 05 Apr '12

05 Apr '12

Hello all, I want to model my protein using template with its ligand bound to it. How can do this..i dnt hv idea. plz help. thnx in advance, Nutan Chauhan Research Scholar Department of Biotechnology BIT, Mesra Ranchi-835215, Jharkhand ________________________________ From: "modeller_usage-request(a)salilab.org" <modeller_usage-request(a)salilab.org> To: modeller_usage(a)salilab.org Sent: Saturday, 24 March 2012 10:27 PM Subject: modeller_usage Digest, Vol 11, Issue 34 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. Re: 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)? (Modeller Caretaker) 2. Re: homology modelling with multiple subunits (Modeller Caretaker) 3. Regarding protein 3D structure modeling (vishal Nemaysh) 4. Re: Regarding protein 3D structure modeling (Modeller Caretaker) ---------------------------------------------------------------------- Message: 1 Date: Thu, 22 Mar 2012 13:44:59 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> To: Valerio Lupperger <valerio.lupperger(a)gmx.net> Cc: modeller_usage(a)salilab.org Subject: Re: [modeller_usage] 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)? Message-ID: <4F6B8F4B.6020705(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 3/22/12 8:08 AM, Valerio Lupperger wrote: > 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? If you can do it in a Python script, you can generally do it with the C API (most of the Python interface to Modeller is simply calling the C API underneath, in the _modeller module). So you can write the equivalent Python code, and then look at Modeller's Python interface to see what the equivalent C API functions are that it's calling. For example, to calculate the energy you would call the energy() method in the selection class; if you look at modlib/modeller/selection.py you'll see that that method calls the C API mod_energy() function. In C you will have to manually keep track of memory and handle errors, of course, which is done automatically for you by the Python interface. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Thu, 22 Mar 2012 13:48:48 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> To: "Zumot, Elia Nabil" <enz1(a)pitt.edu> Cc: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> Subject: Re: [modeller_usage] homology modelling with multiple subunits Message-ID: <4F6B9030.60402(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 3/22/12 10:53 AM, Zumot, Elia Nabil wrote: > 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). Unless I don't understand your question, this is covered by http://salilab.org/modeller/9.10/manual/node28.html Modeller is not going to magically determine the interface region between your subunits and dock them, of course. You need to give it information about the interface between subunits (either by giving it a multimeric template, or by supplying it with subunit-subunit restraints if you only have monomeric templates). Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 3 Date: Sat, 24 Mar 2012 11:27:49 +0530 From: vishal Nemaysh <vishal.bioinfotech(a)gmail.com> To: modeller_usage(a)salilab.org Subject: [modeller_usage] Regarding protein 3D structure modeling Message-ID: <CALCM-RALrVh0c_NhOOVBKU_XvMQiFnnkyi-=18+1qHgasQWrJQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" 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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