Structure analysis for chain number   1

- Sequence of this chain : 

      IRLVFHDSIA ISPAMEAQGK FGGGGADGSI MIFDDIETAF HPNIGLDEIV
      KLQKPFVQKH GVTPGDFIAF AGAVALSNCP GAPQMNFFTG RAPATQPAPD
      GLVPEPFHTV DQIINRVNDA GEFDELELVW MLSAHSVAAV NDVDPTVQGL
      PFDSTPGIFD SQFFVETQLR GTAFPGSGGN QGEVESPLPG EIRIQSDHTI
      ARDSRTACEW QSFVNNQSKL VDDFQFIFLA LTQLG

- This chain was modelled using 3 templates :

  Template          Alignment (Clustalw format)     Secondary information (Sov)     Identity 
   pdb1bek_0          alignment_1_1.aln                    71.0%                     18.5%
   pdb1bep_0          alignment_1_2.aln                    71.0%                     18.5%
   pdb1ccl_0          alignment_1_3.aln                    69.2%                     18.1%

- Template at each amino acid position :

- Deviation between templates on this chain (Angstrom) :

                      1bek   1bep   1ccl
          1bek        0.00   0.11   0.22
          1bep        0.11   0.00   0.21
          1ccl        0.22   0.21   0.00

     . mean deviation :   0.181526
     . superimposed pdb file : super_temp_1.pdb
     . local deviation along chain sequence : jpeg  text
          (Reference : Amino acid model numbering)

In this example, templates share only 18% identity with the query, but the secondary structure agreement is quite good (70%) so it’s reasonable to make a molecular modelling with this  template (see geourjon et al., 2001).  We choose to conserve the 3 templates, even if for 1ccl the Sov value is low (it’s why line is written in red). Using 3 templates gives more flexibility than with only 1 template, but at the opposite that may introduce conflicts, so use modelling multi-templates selection carefully :

v    You need to confirm this selection, and launch Geno3D computing after enter your E-mail. Geno3D job will be running as soon as possible, depend my on computer server availability (you will receive a mail when your job is starting).

v    If you want to change the template choice, you go back and select another.

ü     distances and dihedral angles restraints calculated from the alignment (generated by PSI-BLAST) with templates 3D structure are applied onto on the query sequence. For gaps, statistical restraints are used.

ü     this restraints are used as input for CNS software (Brunger, A.T., Adams, P.D., Clore, G.M., Delano, W.L., Gros P., Grosse-Kunstleve R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T. & Warren G.L. Crystallography & NMR : A new software suite for macromolecular structure determination. Acta Cryst., 1998, 54, 905-921)

ü     the output are 3D models that satisfy theses restraints as well as possible.

ü     at the end of the molecular modelling process you receive a mail which provide an internet address to molecular modelling results (available for seven days). You can use this result via internet or download an  archive file (archive.tar.Z) for analyse results locally on your computer also via a Web interface. This archive must be uncompressed with command :

v    on Unix : zcat archive.tar.Z|tar -xvf -

v    on PC (windows) : with WinZip software (shareware available for example on tucows server : www.tucows.com)

v    on Mac : with Stuffit expander software (Freeware available for example on tucows server : www.tucows.com)

ü     On the server, the main page is :

From this page you can download individual model generated, so you can display this 3D model using a software as rasmol (Freeware available at ). You can also retrieve to some information about modelling process :

v    file report.txt : Information about whole molecule, ie information about energy, Ramachandran diagram (computing using PROCHECK software by Roman A. Laskowski, deviation between models, number of restraints deduce from template, and number of restraints which aren’t respected in models (violations). When a parameter is not satisfactory the line is written in red color.

model  1 :   -8850.40 model  2 :   -8712.33 model 3 : 2859.57 Energetical value You can select model 1 or model 2	Model1 Model2 Model3 Model1  0.00   1.20   1.29 Model2  1.20   0.00   1.24 Model3  1.29   1.24   0.00 Deviation between models on CA (rmsd in Angstrum) ------------------------------------------- Model1 91.2 Model2 91.3 Model3 94.3 Ramachandran repartition (% percent of residus in favorable region)
Superposition of 3 models generated	Restraints repartition	Violations repartition

v    file report_1.txt (and for a dimmer report_2.txt) : Information about each chain, ie deviation between models on this chain, number of restraints deduced from template, and number of restraints which aren’t respected in models (violations). Deviation between this chain and template used to build this chain.

      1bep Mod1 Mod2 Mod3
1bep  0.00 1.38 1.23 1.46
Mod1  1.38 0.00 1.20 1.29
Mod2  1.23 1.20 0.00 1.24
Mod3  1.46 1.29 1.24 0.00

Deviation between one template and models

 --------------------

Superposition (left figure):

- Red : template pdb1bep
- Yellow : Heme (from pdb1bep)
- Blue : model 1 to 3

Illustrations of analysis tools usage :

1 Using some templates for modelling the same protein chain. For example when a protein region was unresolved in a 3D structure, but resolved in another structure.

Future developments :

-        Modelling of dimers  

-        Include ligand in molecular modelling process  

-        Upload personal alignment