November 2020 - modeller_usage

Query regarding the modelling of a particular set of residues in a protein
by Sruthi Sudhakar 20 Jan '21

20 Jan '21

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Fwd: model structure of IDP regions
by Priya Dey 25 Nov '20

25 Nov '20

From: "Priya Dey" <pdey(a)chemistry.du.ac.in> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Tuesday, November 24, 2020 3:37:57 PM Subject: model structure of IDP regions espected sir/ madam i want to model the unmodelled region of an intrinsically disordered protein region. I have tried the basic modelling tutorial with the total sequence of idpr 1mvf and the coordinate of the ordered region of the 1mvf idpr. But the final modelled structure generated have only the coordinate of the ordered one. Please guide me, so that i can find the all region coordinates of the modelled structure of 1mvf. Thanking you Priya dey Research Scholar Department of Chemistry University of Delhi

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MODELLER modelling of a single chain
by Austin Varela 25 Nov '20

25 Nov '20

Hello, I have a PDB file containing a complex composed of 2 proteins interacting. I wish to perform homology modelling of one of these proteins and leave the other one fixed. I have been able to do the modelling of the one protein of interest, however I am not sure how to have MODELLER include the fixed protein in the final PDB outputs as all my current outputs only contain the modelled protein. Is this some option I can modify on running MODELLER? Or would I have to align the new structures to the old one and somehow merge files to reintroduce the other protein. Thanks for the help! Austin -- Austin Varela University of Rochester - Class of 2020 BS Computational Biology & BA Data Science Computational Biology Researcher in the Werren Lab

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multi-chains: modeled separately or jointly?
by Amin Zia 25 Nov '20

25 Nov '20

Hi List, In multi-chain modeling, I am wondering if the alignment and modeling algorithms take into account multiple chains and their spatial locations concurrently or just simply model each chain separately and then combine the results. Related to this, is the dope score assessment a sum of scores for chains in these cases (in which case, it's assumed the statistics are measuring two independent models), or the correlation of chains are considered in the statistical assessment? Thank you in advance Amin Zia, Stanford Immunology

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