November 2014 - modeller_usage

alpha-helix
by Juan Munoz-Garcia 24 Nov '14

24 Nov '14

Dear Modeller users, I’ve tried to make an alpha helix from the peptide sequence (21 amino acids) using the script shown in the website (http://www.salilab.org/modeller/wiki/Make%20alpha%20helix) i.e., imposing restraints to force the alpha helical structure. I’ve tried with conjugate_gradients, molecular_dynamics and quasi_newton methods, but the output just showed a helix for a small part of the peptide, showing a coil for the rest of it. Although this is providing some information itself, and it roughly agrees with experimental data, I do want to force an alpha helical structure for the whole peptide. Do you know how this can be done? I was wondering if there is any method to grow an alpha helix just based on the backbone and once formed growing the side chains from it, thus avoiding possible highly destabilising side chain - side chain interactions precluding the helix formation. Regards. Juan C.

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Modelling loop region in homodimer
by aneesh cna 14 Nov '14

14 Nov '14

Drear members, I am a new comer to modeller. I am trying to model a ~15AA long missing loop region in a homo-dimer. Both monomer units in the homo-dimer missing the loop region. Unfortunately, my template is a monomer unit. How can I model the loop region in both monomer together.? I have tried modelling each monomer units separately, since the available template was a monomer. But, when I built the dimer from the modelled monomers (just by putting the modelled monomers together in a pdb file) the loop in one of the monomer got interlocked within a helix of the second monomer. Is there a different way to model the loop here? Many thanks in advance Regards Anu

2 1

Modelling loop region in homodimer
by aneesh cna 11 Nov '14

11 Nov '14

Drear members, I am a new comer to modeller. I am trying to model a ~15AA long missing loop region in a homo-dimer. Both monomer units in the homo-dimer missing the loop region. Unfortunately, my template is a monomer unit. How can I model the loop region in both monomer together.? I have tried modelling each monomer units separately, since the available template was a monomer. But, when I built the dimer from the modelled monomers (just by putting the modelled monomers together in a pdb file) the loop in one of the monomer got interlocked within a helix of the second monomer. Is there a different way to model the loop here? Many thanks in advance Regards Anu

1 0