February 2010 - modeller_usage

Modeling a larger protein with multiple templates
by nornik 08 Feb '10

08 Feb '10

Hello I have sent this query before, but noone replied so I will send it again, hoping for some assistance. I am wondering if anyone can help me with this problem I have. I am modeling a large protein and I am using five different templates on different regions of the protein. Let's say the alignment looks like this: MMMMMMMMSMMMMMMMMMMSMMMMMMMMMMMMMMMMMMMSMMMMMMMSMMMMMMMMMSMMMMSMMMM Model AAAAAA----------------AAAAAAAAAAAAAA-------------AAAAAAAASAA------- core template ----BBBBSBBBBBBB---------… [View More]

2 1

Conversion of L-isomers to their D-isomeric form
by abdullah ahmed 04 Feb '10

04 Feb '10

Bonjour, I have a protein in PDB format that I have used successfully, to make a model (using the command "a.very_fast()"). However, whenever optimization is carried out (even by the default optimization in "model-full.py") some of the residues convert to their D-isomeric form. To avoid this I have tried the following: Making a series of models rather than just one to avoid problems caused by randomization. Turning randomization off using the "deviation=None" command in the "allhmodel" … [View More]

2 1

Re: [modeller_usage] should I use T-COFFEE alignment or generate one with alignmnent() module
by Thomas Evangelidis 04 Feb '10

04 Feb '10

Actually I used compare.py as a means to narrow down the list with the 8 potential templates, not to generate an alignment for comparative modelling. As for the consensus alignment (48 sequences and templates in total), it looks very good, all the conserved motifs from each sequence coincide. The problem is that sequence matches not necessarily imply structure matches, something that was denoted by malign3d when I fed the 8 template sequences as they were aligned in the consensus alignment. … [View More]

2 1

should I use T-COFFEE alignment or generate one with alignmnent() module
by Thomas Evangelidis 03 Feb '10

03 Feb '10

Dear Modellers, I have a protein domain with very low sequence identity to PDB structures (37%), therefore I created a nice consensus alignment with T-COFFEE which includes both sequences and templates. After carefully inspecting the alignment, discarding bad matches, and realigning, I ended up with 8 potential templates which all look good to me. Thus I tried to adapt the compare.py script used in the basic tutorial, to help me select the best templates. Initially I tried to feed my … [View More]

2 1

docking and modeling peptid.
by Knut J Bjuland 03 Feb '10

03 Feb '10

Hi Can the latest version of modeller do docking of a peptide into an active site. In case modeler can not do this kind of docking, which particular program is best suited for doing peptid protein docking. Knut J _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969

2 1

Amino acid Isomers
by abdullah ahmed 02 Feb '10

02 Feb '10

Hello, My question is related to optimization. I increased the default optimization in "model-full.py" using the following code: # High VTFM optimization: a.library_schedule = autosched.slow a.max_var_iterations = 5000 Optimization does occur, however a few amino acids are changed from their L-isomeric forms to the D-isomers. To check if this was caused by problems with the PDB file I was using, I used a file(2KDV) from the protein databank. The same thing happens to it as well. Also if a … [View More]

2 1

MOULDER protocol
by frank peelman 02 Feb '10

02 Feb '10

Dear all, Is/are the MOULDER protocol (s) available for local use ? kind regards, Frank

2 1