Geno3D – release 2
aim of Geno3D server is to make accessible to all biochemists and biologists an
automated protein modelling Web server to generate protein 3D model. This server
is available in the hope that it will be useful, the entire risk as to the
quality and performance of the server is with you.
The result is only a model and must be considered carefully, it isn’t
an experimental 3D structure!
Improvement from release 1 :
non-redundant proteins sequences database are available.
Possibility to select
template whit low identity level (until 20%, use it carefully).
Use prediction of
secondary structure agreement to validate template selection and alignment (Geourjon, C., Combet, C., Blanchet, C. &
Deléage G., 2001, Identification of related proteins with weak sequence
identity using secondary structure information. Protein science, 10: 788-797).
Availability of model
analysis tools in Web interface
All files are included
in archive file which can be download for local use.
superposition file with template ligand (geometrical position deduce from
Availability and limitation in Geno3D :
is available :
At URL : http://geno3d-pbil.ibcp.fr
Geno3D Web server is provided and developed by "PBIL
Lyon-Gerland" team. There are no restrictions on its use by non-profit
institutions. Usage by and for commercial entities requires a license agreement
Geno3D server release 2 generates model until
500 amino acids.
default the modelling process is made using :
Database : NPSA 3D SEQUENCES AT 100% HOMOLOGY (from
Until 3 run for similarity search with PSI-BLAST
Generation of up to 3 models
strategy used in Geno3D is comparative protein structure modelling by spatial
restraints (distances and dihedral) satisfaction.
is most frequently used for homology or comparative protein structure modelling
the user provides sequence to be modelled (query)
which is compared using PSI-BLAST method (Müller,
A., MacCallum, R.M., and Sternberg, M.J.E. 1999, Benchmarking PSI-BLAST in
genome annotation. J. Mol. Biol. 293:
against a protein sequence database issue from PDB (all entries by default).
the user selects PDB entries as templates for
molecular modelling. In this case, 1bep, 1ccl and 1bek are selected.
ü for each template Geno3D server computes secondary structure prediction, display percent of agreement in secondary structure (geourjon et al., 2001), repartition of information from template on query sequence. In case of selection of multi-template the rmsd (root mean square deviation) between templates on carbon alpha is also displayed :
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
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)
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 :
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).
If you want to change the template choice, you
go back and select another.
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.
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,
the output are 3D models that satisfy theses
restraints as well as possible.
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 :
on Unix : zcat
archive.tar.Z|tar -xvf -
on PC (windows) : with WinZip software (shareware
available for example on tucows server : www.tucows.com)
on Mac : with Stuffit expander software (Freeware
available for example on tucows server : www.tucows.com)
ü On the server, the main page is :
WHOLE MOLECULE (energy, ramachadran, ...) : report.txt
ABOUT EACH CHAIN (deviation, restraints, comparison with each template...) :
- Chain 1 : report_1.txt
SELECTION : valid.txt
ARCHIVE FOR LOCAL ANALYSIS : archive.tar.Z
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
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
models on CA
Superposition of 3 models generated
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
1bep Mod1 Mod2 Mod3 1bep 0.00 1.38 1.23 1.46
Deviation between one template and models
Superposition (left figure):
- Red : template pdb1bep
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
In pdb1jsq structure 2 regions are unresolved (in yellow color 207-238
and 343-420). The second
region correspond to the “ATP binding domain” has been resolved in a
structure of a homologous protein (code pdb1jj7). So using this two
templates, it is possible to built a model for an ABC tranporter family
Future developments :
Modelling of dimers
Include ligand in
molecular modelling process