Difference between revisions of "Homology modeling fallback data"
| Line 14: | Line 14: | ||
QGTWIPLEQGRALAQRNNIYDRLRPIF | QGTWIPLEQGRALAQRNNIYDRLRPIF | ||
| − | ==FASTA formatted alignment== | + | ==FASTA formatted target-template alignment== |
>1MB1 sequence from coordinates 3..100 | >1MB1 sequence from coordinates 3..100 | ||
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---------------------HVMRRREDNWINATHILKAAGFDKPARTR | ---------------------HVMRRREDNWINATHILKAAGFDKPARTR | ||
ILERDVQKDVHEKIQGGYGKYQGTWIPLEQGRALAQRNNIYDRLRPIF | ILERDVQKDVHEKIQGGYGKYQGTWIPLEQGRALAQRNNIYDRLRPIF | ||
| − | |||
| − | |||
==SwissModel response== | ==SwissModel response== | ||
Revision as of 13:31, 31 October 2007
Please remember: if you use information from this page as a fallback for technical problems with the assignment, you must document this in your submission. State what you tried, what didn't work and only then use the data from here.
Contents
Target sequence
>MBP1_CHAGL XP_001224558:33..108 HVMRRREDNWINATHILKAAGFDKPARTRILERDVQKDVHEKIQGGYGKY QGTWIPLEQGRALAQRNNIYDRLRPIF
FASTA formatted target-template alignment
>1MB1 sequence from coordinates 3..100 NQIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTR ILEKEVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLF >MBP1_CHAGL XP_001224558:33..108 ---------------------HVMRRREDNWINATHILKAAGFDKPARTR ILERDVQKDVHEKIQGGYGKYQGTWIPLEQGRALAQRNNIYDRLRPIF
SwissModel response
Four e-mails are sent by SwissModel after submission of the modeling request. Two of the received files are welcome and help messages. Two other e-mail messages conatin the program output and the model.
LGA superposition
The resulting output produced by the LGA server for the 1DUX_ABC and 1MB1 superposition consists of two parts: the superposition report explains which residues were matched and what their RMSD after superposition was. The coordinates contain the rotated coordinates of the entire 1DUX file superimposed on 1MB1. In order to use this for as RasMol, the following manual edits were performed.
- LGA created several
ENDrecords in the middle of the file. These prevent the following lines to be read in. They were simply deleted. Since the protein chans of the Mbp1 and Elk-1 domains are closely superimposed, RasMol tries to draw multiple bonds between the residues that have close contacts. This was addressed by bracketing the chains inMODELandENDMDEL, which prevents bonds between being drawn.
- LGA created several
Protein-DNA complex model
The DNA coordinates (chain A and B) from the LGA superimposed coordinate file were copied, and pasted into the SwissModel coordinate file, thus generating a homology model of a Protein / DNA complex.
