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Help on format of file Sample custom potential file
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Help on format of file Sample residue mutation file
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Four letter PDB complex code or upload file in PDB format.


Job Parameters

Got It
Parameters with help content are in bold face.
The jobname is chosen by the user for the job. Jobname is useful when the user wants to distinguish between the different submitted job(s).

If the user provide an email address then an email notification will be sent to inform the user about the job completion or unexpected termination of the job.

It is advised that a valid and active email address must be provided to receive notifications about the job status.

PDB Structure

The PDB structure is the primary input to the server. The PDB structure can be specified in the following ways:

1. By writing the four letter valid PDB complex code
2. By uploading a valid PDB file.

Caution: If a wrong PDB code is entered or if the uploaded file is not a valid PDB file then the job will be rejected by the server and the user will be informed of the respective error.

Mutational Analysis

Amino acid residues on the interface are mutated in-silico and the interfaces rescored to estimate the contribution of individual residues towards the interface. The user is presented with three options in this regard.

Option Requirement
Interface Alanine Scanning This option will mutate all the interface residues to alanine.
Interface Saturated Mutagenesis This will do a saturated mutagenesis for all the interface residues.
Manual mutation specification: This option allow to manually specify the residues to be mutated. Further, user can mutate specific interface residue to other residue(s), to alanine or do a saturated mutagenesis for the selected residue.

A a sample mutagenesis file is also provided to illustrate how different type of mutations can be specified by the user. Each line of the file has two tab separated fields.
Mutation Type Field 1 Field 2
Mutating the residue to Alanine
(mutate the residue number 177 (valine) in chain 'B' to Alanine)
Mutating a residue to every other residue
(mutate the residue number 20 (histidine) in chain 'A' to all the other residues, Saturated mutagenesis)
20:HIS:A *
Mutating the residue to specific residue
(mutate residue number 27 (gultamate) in chian 'A' to lysine)
Mutating the residue to a list of residue
(mutate residue number 27 (gultamate) in chian 'A' to lysine and valine)
Description of Output The most important residues are listed in a ranked order list. The last column 'Score-Diff' shows the magnitude of change in scores upon mutagenesis. The positive values of this column imply that the mutation destabilizes the interface whereas negative values imply that the mutation stabilizes it.

Distance Threshold

Two amino acid residues are defined as interacting if any relevant atom of residue A was within any relevant atom of residue B. The user can specify different distance thresholds for defining interface residue contacts and choose between 4 Å, 6 Å and 8 Å.

Note: A smaller distance threshold will provide a more stringent definition of the interface whereas a larger threshold might be helpful in the case of a loosely binding complex.

Interacting Atoms(s) Type

This parameter is useful when certain types of interactions are dominant in the protein complex.

The users can choose to isolate interactions between certain atoms and use those to define the interface. Choices for this parameter include side chain-side chain interactions, main chain-main chain interactions and main chain-side chain interactions.

Our server makes use of 48 different statistical potentials that have been constructed using a combination of different interaction distance thresholds and type of interacting atoms. Based on the input parameters given by the user, a particular statistical potential will be used and the corresponding Z-score threshold be employed to make the prediction.

Custom Potential
Using this option, the user can upload their own statistical potential and use it for testing.

Format for custom potential file
The custom potential file consists of two comma-separated fields. The amino acid pairs represented by three-letter codes (ex. ALA-ALA) form the first field and their corresponding potential values form the second field. Each residue-pair and its potential value occupy a separate line. Below is an example of how the entries in the file should look like
ALA-ALA, -3.809
ALA-ARG, -3.044
ALA-ASN, -2.725
ALA-ASP, -2.474
ALA-CYS, -2.11
ALA-GLN, -3.029
ALA-GLU, -2.759
ALA-GLY, 0.0
ALA-HIS, -3.192

For details, a sample file is provided here: Custom Potential File
Specific Interface
By default, all the interfaces in a multimeric query structure are scored. To generate predictions about a particular interface only, the user can specify the interface using this parameter. Specifying the interface of interest can significantly speed up computation times.

For example, user can specify only chain A (as interface 1) and chain B (as interface 2) and look at the residue interactions on these interfaces.

Processing your request.