Homology Modeling Part-II - assigned 11/12/08

You are to make a homology model of two more phospholipase A2 enzymes using the Swiss-Model server and the program  Modeller.   The targets are the human form of the following sPLA2.  If you cannot find the human sequence, it is OK to use the mouse sequence.  We will do the random drawing in class to see which two you'll be assigned.

Targets:  IIC, IIE, IIF, III, V and XII

Templates exist for the following:  IA, IB, IIA, IID,  and X

1) You will make models of the two targets assigned.  You need to assess whether it is better to use a single "best template" approach, or if it is better to model from multiple templates for each of your particular targets.  You are also expected to make your models with both Swiss Moldel and Modeller.  Make sure you thoroughly explain your choice of templates used for the modeling assignment.  

2) For each of your two tartgets to be modelled, prepare a multi- protein sequence alignment of your choice of templates aligned with the target sequence.  So this means you need to do this step twice, as each target is likely to have a different set of templates.  You could use the programs ClustalW/Boxshade (demonstrated in class) or other program.  In addition to turning these in for each target modelled, you should use this approach to help make decisions of what templates to include (part 1).

3) You will be depositing your models into a folder in your pingouin.chem.udel.edu account.  No need to e-mail me your pdb files anymore. 

4) Here's where you can be creative.  I want you to compare each of your two modeled targets to the other know sPLA2 structures.  In class we can brainstorm ideas of what this comparison should involve.  

5) Pick one of your modeled sPLA2 targets and compare the model to what is known about the function of the particular sPLA2 protein.  This is an important step is assessing the accuracy and utility of a comparative model.  Again, this is where you can really show your creativity, as there will be no single correct answers here.

Usefull Links
ExPASy  - http://ca.expasy.org/
PDBBLAST - http://protein.cribi.unipd.it/pdbblast/
Swiss-Model  - http://swissmodel.expasy.org//SWISS-MODEL.html
NCBI PubMed - http://www.ncbi.nlm.nih.gov/sites/entrez/
Deepview - http://spdbv.vital-it.ch/
Deep View Tutorial - http://www.usm.maine.edu/~rhodes/SPVTut/index.html
PyMol - http://pymol.org/
Protein Data Bank - www.pdb.org/
Principles of Protein Structure, Comparative Protein Modeling and Visualisation
CLUSTALW - http://www.ebi.ac.uk/clustalw/
BOXSHADE - http://www.ch.embnet.org/software/BOX_form.html
Biology Workbench - http://workbench.sdsc.edu/ 

 

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