Practical Guide to Homology Modeling: Difference between revisions
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There are many superb molecular graphics programs. Most are quite challenging to use ("not user friendly"). | There are many superb molecular graphics programs. Most are quite challenging to use ("not user friendly"). | ||
''FirstGlance in Jmol'' is perhaps easiest to use, has a great deal of help for interpreting what you see, and is quite powerful. (See [http://bioinformatics.org/firstglance/fgij/whatis.htm What Is FirstGlance in Jmol?].) | ===FirstGlance in Jmol=== | ||
''FirstGlance in Jmol'' is perhaps easiest to use, has a great deal of help for interpreting what you see, and is nevertheless quite powerful. (See [http://bioinformatics.org/firstglance/fgij/whatis.htm What Is FirstGlance in Jmol?] and [[FirstGlance in Jmol]].) | |||
*Download your homology model(s). | |||
* Go to [http://firstglance.jmol.org FirstGlance.Jmol.Org]. | |||
* Click on ''Upload your own PDB file'' and designate your homology model. Click ''View in FirstGlance''. Your molecule should appear momentarily. | |||
====Hydrophobic/Polar==== | |||
Most of the views under the ''Views'' tab will be informative. Particularly important is the ''Hydrophobic/Polar'' view. Soluble proteins should not have large areas (> ~ 15 Å across) of hydrophobic surface. Polar residues should be sprinkled over the entire surface. An exception is lipases, e.g. [[1lpm]], where the pocket at the catalytic site is hydrophobic. | |||
==See Also== | ==See Also== | ||
