OPRA Server

FAQ and Help


Tutorial

There is a OPRA server tutorial which you can follow here.


Input data

OPRA server uses the PDB file of the protein which RNA-binding sites predictions you want it to determine:

  1. Protein PBD structure. PDB file.

Email address

The email address is only used to notify the user once the job has been finished, but it is required to be from an academic institution. If your email address is not identified by our server, please use the contact section to notify this issue in order to add your institution to our database of valid academic centers.


Reference

To cite OPRA server, please reference “OPRA server: a rigid body protein-protein docking server, B Jiménez-García, C Pons, DI. Svergun, P Bernadó and J Fernández-Recio, 2014 (submitted).”


PDB structure files

We encourage to follow the PDB file format. Note that incomplete backbone or side-chain atoms may incur in inaccurate results and/or software failure.


Result files

Once the computation has ended, the server prepares a gzip compressed tar archive containing several result files organized by folders in the following way:

Note: "[xxx]" is a numeric identifier

input_data

This folder contains the original data provided by the user.

OPRA_results

This folder contains the files generated by OPRA server:

  • project_[xxx].pdb: PDB file parsed by OPRA server.
  • project_[xxx].pdb.H: PDB file parsed by OPRA server in which the hydrogen atoms automatically added by OPRA server have been included.
  • project_[xxx.pdb.opratab: OPRA server output results file. This file has the following format:
    Example:
    Res           Potential   OPRAradius    OPRAvalue
A.ILE.16          0.007       21.000       -0.830
A.VAL.17          0.021       21.000       -0.927
A.GLY.18         -0.059        9.000       -0.599
A.GLY.19         -0.044       21.000       -0.671
A.TYR.20         -0.033       21.000       -0.594
A.THR.21         -0.002       17.000       -0.299
A.CYX.22          0.044       17.000       -0.205
A.GLY.23         -0.035       21.000       -0.134
A.ALA.24          0.104        5.000        0.072
A.ASN.25         -0.042        5.000       -0.106
A.THR.26         -0.002        9.000       -0.030
A.VAL.27          0.022       21.000       -0.405
...
    Where the different columns represent:
    • Res: Residue Id.
    • Potential: Residue potential. Corresponds to the residue statistical potential times its relative ASA (Accessible Surface Area). For a detailed explanation, please, refer to Materials and Methods section of the original paper.
    • OPRAradius: Residue radius. Corresponds to the radius of the patch considered for computing the residue OPRA value. For a detailed explanation, please, refer to the Materials and Methods section of the original paper.
    • OPRAvalue: Residue computed OPRA value.
  • project_[xxx].pdb.opra: PDB file parsed by OPRA server in which the computed OPRA values have been included in the 'Temperature factor' field (columns 61-66). This file may be helpful if you want to represent, with a third party application, the computed OPRA values graphically, coloring each residue of the protein according to its OPRA value.