July 2014 - modeller_usage

Auto Response
by Filipe Natalio 29 Jul '14

29 Jul '14

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Modeller 9.14 release
by Modeller Caretaker 29 Jul '14

29 Jul '14

The new version of Modeller, 9.14, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.14 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.14 is primarily a bugfix release relative to the last public release (9.13). Major user-visible changes include: # The new PDB format (PDBx/mmCIF) is … [View More]

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Advanced clustering
by James Starlight 23 Jul '14

23 Jul '14

Dear modeller users! I wounder if it would possible to perform advanced clustering of all generated models (e.g using automodel.cluster()) based on the selected criterium from the built models (e.g percent and composition of secondary structure in the selected region, number of salt-bridges in selected region, distance between selected pair of atoms etc). Many thanks for suggestion, James

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Problem regarding 3D structure prediction
by Vishal Nemaysh 22 Jul '14

22 Jul '14

Respected Sir, I have faced a problem during 3D structure prediction of my target protein of interest. The length of the protein sequence is (1106 amino acids). Sir i have tried to find out some templates for covering the whole query sequence during BLAST or psiBLAST. But there is no any single template or multiple templates are found to occupied this whole query sequence. Kindly suggest me how to overcome this problem. Thanks in advance. -- Vishal Research Scholar, Neuropharmaceutical … [View More]

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Join me on LinkedIn to share updates and stay in touch
by Jayashankar Selvadurai 22 Jul '14

22 Jul '14

Hi , I'd like to add you to my professional network on LinkedIn. - Jayashankar Accept: https://www.linkedin.com/e/v2?e=-xaf1me-hxx2izlh-6y&a=preRegInvite&tracking… You are receiving Invitation emails. Unsubscribe here: https://www.linkedin.com/e/v2?e=-xaf1me-hxx2izlh-6y&t=uns&midToken=AQFmrFVh… Learn why we included this at the following link: http://www.linkedin.com/e/v2?e=-xaf1me-hxx2izlh-6y&a=customerServiceUrl&ek=… © 2014, LinkedIn … [View More]

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Protein:Protein complex PIR format
by Parker de Waal 15 Jul '14

15 Jul '14

Hello MODELLER users, After looking through the mailing list I have been able to find numerous discussions about protein:protein complex homology modeling, however I have been unable to find any examples for proper PIR formatting and was wondering if someone would be willing to help. I would like to perform modeling for unknown complex A2:B1 where A1:B1 is known and while holding B1 completely frozen. Would the following PIR snippet below work for such modeling or is more information required … [View More]

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conjugate gradients or molecular dynamics optimizations with automodel.make()
by Li SUN 15 Jul '14

15 Jul '14

Hi everyone, I have a question regarding the usage of automodel.make() for modelling a protein structure from known structures. Does this function include optimization methods e.g. conjugate gradients or molecular dynamics so that it will output a structure close to the native state (lowest-energy state), or do I have to call conjugate_gradients() or molecular_dynamics() explicitly after automodel.make() to do an energy minimization? Thanks in advance. -- Li Sun Department of Physics … [View More]

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Mismatch in the alignment
by Sajeewa Pemasinghe 07 Jul '14

07 Jul '14

Hi everyone, I am trying to fill 11 missing residues in a protein. 5 of them are at the N-terminal and the other 6 are at the C-terminal. Other than that there are 9 non-standard residues and 228 waters in the pdb as well. My alignment file looks as below. >P1;2ABC structureX:2ABC: 6 :A:+402 :A:MOL_ID 1; -----PRFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYG TNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAARLAVGCVVELVFKVATGELKNGFAVVRP … [View More]

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Structuropedia
by Amjad Farooq 01 Jul '14

01 Jul '14

Hi everyone, Here is a new web interface that may be of interest to some of you: http://structuropedia.org This is a simply yet powerful and versatile web interface with capabilities for modeling and rendering of proteins alone and in complex with peptides and DNA. Powered by a wide array of engines including Biopython, Blast, Clustal, JSmol, Modeller, RefSense and VMD. Any feedback will be most welcome. With warmest regards, *AMJAD FAROOQ PhD DIC | Associate Professor*Dept of … [View More]

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