This site is a fork of the original PRABI Geno3D server

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May 3rd, 2024: Geno3D updated (see NEWS).

The user provides a query sequence in Geno3D's input form and sets PSI-BLAST search parameters against a database of protein sequence with known 3-D structure found in the Protein Data Bank (PDB).

After the PSI-BLAST search, the user can select one or multiple templates in the result table.
N.B.: in this screenshot, three templates with low sequence identity (<25%) with the query were selected in order to illustrate the use of predicted secondary structure agreement (Sov parameter) in template selection (see below).

To validate the template selection, the Sov parameter is computed with predicted secondary structure between each template and the query if their pairwise identity is <25%.
The coverage between template(s) and query is displayed as a graphic. Moreover, when multiple templates are selected, the carbon alpha root mean square deviation (RMSD) between templates is computed too.
N.B.: High/low values that need to be taken with caution are highlighted in red.

Then, the user can submit the model computation after adjusting modelling parameters (e.g. number of models, number of restraints) and entering an e-mail address.

After computations, the user receives one e-mail and can access the result page allowing:

• to download computed models in PDB format for visualization with client software like PyMOL or ChimeraX
• to analyze all models or individual chains (energy, Ramachandran diagrams, RMSD, superimposition, restraint distribution and violations)
• to download an archive with all the files (.tar.gz)

Geno3D is able to provide 3-D models of a protein in complex witha ligand (in yellow below, files minim-hetatm_*.pdb) when the template (e.g. PDB 1BEP in this example) has been solved with it.

Geno3D is able to compute oligomers when a template of the oligomeric form has been solved. For such a modelling, you can contact us.

Example query sequence:

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

References.

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