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:
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 an archive file (.tar, .tgzi, .zip, .bz2 or .tar.gz) for analyzing multiple structures at the same time (i.e. models derived from docking simulations)
Specify the chains
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 be used instead of the autogenerated one.
Email
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 ouput 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 repositoy.
The link to the repository can be found at the BonvinLab software page.