Manual
PRODIGY (PROtein binDIng enerGY prediction) is a web application to predict the binding affinity of protein-protein complexes based on intermolecular contacts.
Input
- The protein-protein complex
- PRODIGY server takes as input the three-dimensional structure of the protein-protein complex in PDB or mmCIF format:
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You can choose one of the following options:
- upload the 3D structure coordinates in PDB or mmCIF format - provide a protein databank ID code for automatic retrieval from the Protein Data Bank - Upload a multi-model PDB ensemble or .zip file with multiple structures to analyzing multiple structures at the same time
(i.e. models derived from docking simulations) - Specify the chains
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The user is required to specify the chain identifiers for the molecules involved in the interaction.
Interacting molecules associated with multiple chain IDs should be provided as comma-separated list.
For the FAB/HIV-1 capsid protein p24 complex (PDB code 1E6J) the input would be expected in following format:Interactor 1: P Interactor 2: L,H In this example, the binding affinity will be predicted for the interface made between chain P (p24) and chains L and H (FAB).
- Please note! PRODIGY only supports the 20 standard amino acids
- Archive file
- When submitting an archive file to PRODIGY, make sure that the chain IDs of ALL structures are compatible with the Interactors specified in the submission form.
Parameters (optional)
- Temperature (in ℃)
- By default the value of the dissociation constant (Kd) is calculated at 25 ℃. The user can change this value to any desired temperature.
- Job ID
- The user can specify a personalized Job ID to identify the run.
- If an email is provided, a link with the results will be sent when the job is done. The results will be stored for 2 weeks.
Output
PRODIGY outputs are displayed online and remain downloadable for 14 days. A link to the online resource is also emailed to the user, if an email is provided.
The results returned by the server include:
| 1. | Predicted value of the binding affinity (ΔG) expressed in kcal mol-1 |
| 2. | Calculated value of the dissociation constant (Kd) at a given temperature (25 ℃ by default), expressed in Molar (M) |
| 3. | Number of intermolecular contacts (ICs) at the interface within the threshold distance of 5.5 Å, separately listed according to the contact property |
| 4. | Percentage of the charged and apolar non-interacting surface (NIS%) of the complex |
| 5. | Downloadable table (.txt) listing the residues in contact within the given threshold |
| 6. | Downloadable ready-to-run Pymol (Delano Scientific, 2002) script (.pml) with different color coding for the interacting residues |
| 7. | Archive file including all the output files |
How to run PRODIGY locally
In case you have many structures on which you wish to run PRODIGY, we distribute the standalone version in form
of a Github repository.
The link to the repository can be found at the BonvinLab software page.
