April 2013 - modeller_usage

how to build the loop of protein model using modeller
by aixintiankong 03 May '13

03 May '13

Dear, The last email have some errors please see this one. In my system ,the loop is part of the active pocket of the protein. when the ligand is absent, the loop is disordered. if the ligand is present , the loop can transform into helix. In order to simulate the disordered loop transform into helix , i should build a model that the ligand and cofactor are in the disoreded loop site. In my system, there is a NAD+ cofactor in the active site and interact with the ligand.when the ligand and cofactor NAD+ coexist, the disordered loop can transform into helix. In the PDB(protein date base) i find the complex with the liand,NAD+ and the state of the loop is helix. i also find a structure of the protein without the liand, NAD+ and the state of the loop is disordered. The sequences similarity of the two structure is 100% and the RMSD between the two structures of the protein is 0.275 . i don't know how to build a model that the protein, NAD+ and ligand coexsit and the loop of protein is disordered. could give me some advice and tell me how to do it detailed? thank you very much.

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how to build the loop of protein model using modeller
by aixintiankong 29 Apr '13

29 Apr '13

Dear, In my system ,the loop is part of the active pocket of the protein. when the ligand is absent, the loop is disordered and if the ligand is present , the loop can transform into helix. In order to simulate the disordered loop transform into helix , i should build a model that the ligand is in the disoreded loop site. In my system, there is a NAD+ cofactor in the active site and interact with the ligand.when the ligand and cofactor NAD+ coexist, the disordered loop can transform into helix. In the PDB(protein date base) i find the complex with the liand,NAD+ and the state of the loop is helix. i also find a protein structure without the liand, NAD+ and the state of the loop is disordered. The sequences similarity of the two structure is 100% and sturctue the the RMSD bettwen the two protein is 0.275 . i don't know how to build a model that the protein, NAD+ and ligand coexsit,but the loop of protein is disordered. could give me some advice and tell me how to do it detailed? thank you very much.

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How to get specified residue modelling
by Anogna 29 Apr '13

29 Apr '13

Dear friends, I have been struggling from past one week with the following kind of modelling.... I have a target sequence which is 97% identity with two PDB's (named A and B) I just want to make A as main template, but A has some residues missing, so i thought of making B as template for those missing residues in the "PDB A". But to go with this I am not able to get a python script file in which i can specify build residues. Can anyone can help me with this please. Thanking, Anogna

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Fwd: Run Modeller processes on multiple cpus
by Lalith Kumar 20 Apr '13

20 Apr '13

Hi, Greetings.... I am running mod9v11 on Intel Xeon with 12 cores processor. I have found that modeller is utilizing only single processor. Even though there are few older posts regarding the execution of modeller processors on multiple processors, I am unable to implement them. Sorry, I am newbie to python. It will be a great help if you could help me with a script or procedure to set up the running of modeller processes on multiple processors. This will save my lifetime. Please do the needful. Thank you Regards, Lalith -- Lalith Kumar K Research Associate, CADD Division, Dr. Reddy's Institute of Life Sciences (Formerly known as Institute of Life Sciences) University of Hyderabad Campus Gachibowli, Hyderabad 500046, India

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Modelling ofsymetric dimer
by James Starlight 15 Apr '13

15 Apr '13

Dear Modeller users! I want to model simple symmetric model of the TRP-repressor consist of 2 identical chains based on known PDB structure of that protein where some residues from N and C terms are absent in both monomers. Could you provide mewith some tutorial for such simple task ( as the input I'd like to define pdb consisting of the A and B chains as well as sequence of one monomer. As the output I'd like to obtain the same pdb with two chains included with the refined conformations of the N and C unstructured segments). Thanks for help James

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building missing residues
by Mary Varughese 09 Apr '13

09 Apr '13

Hi, a protein i am dealing with has some missing residues. I am trying to build it with modeller. How could i verify the structure generated? Also the remarks says, CA 5% of the side chains are poorly defined and are currently modelled as alanines. Do any one know the meaning of this remark. Should i do any thing as part of correcting the structure for md simulation?

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