Information about the SWISS-MODEL 7TM Interface

Methods

1. Group specific templates:

   Group specific templates (GST's) are generated for a number of selected 7TM receptors for which sufficient relevant mutagenesis data is available. The number of GST's will grow with time, which should ensure an ever increasing model quality.
   The GST structures are generated using Pawel Herzyk's novel simulated annealing Monte Carlo procedure, which orients rigid helices to satisfy structural restraints. The restraints are derived from theoretical considerations of protein structure and from the analysis of:
   • The 2D projection map.
   • Experimental information on native and mutant proteins.
   • Sequences of related proteins.

2. Co-ordinate generation by ProMod:

   The co-ordinates of each helix are generated by the protein modelling tool ProMod.

3. Energy Minimisation:

   Final Energy Minimisation is performed by Gromos96. Only a few cycles are used to improve the stereochemistry of the model and to remove the unfavorable clashes.

Procedure

1. Helix selection

   Use sequence analysis tools to identify the regions that will become the trans-membrane domains of your 7TM receptor.

2. Data input

   1. First select the modelling template you wish to use.
   2. The next "Form" will ask you to provide the central residues for each helix you determined. The number of amino acids in each helix is dictated by the selected template as the residues are matched according to their positions in the helix. These numbers are indicated on the form. Gaps may be inserted at both ends by using dashes (-), but should never disrupt the helix core. You may also provide the actual start residue for each helix, which will facilitate the finding of amino-acids in the structure.
   3. Do not forget to provide a valid E-mail address and a Project title.

Manuel C. Peitsch