Predicting the functional consequences of point mutations in proteins.

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 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 immediately by the server and the user will be informed of the respective error.


MUTATION

This field provides 3 categories to do the mutation:

1. Point Mutation(s): If this option is selected then the user has to provide the positions to be mutated in the 'Specify Mutation(s)' field manually.

2. Alanine Scanning: If 'Alanine Scanning' option is selected then the user has the choice of either mutating all the positions to 'Alanine' (this is also the default choice) otherwise user can also specify positions to be mutated to alanine by writing into the 'Specify position(s)' field ( in this case the default behavior will be overridden).

3.Saturation Mutagenesis: If 'Saturation mutagenesis' option is selected then the user has the choice of mutating all the positions in the specified PDB structure (this is the default behavior) or the user can also specify particular positions to be mutated by writing the positions in the 'Specify position(s)' field.


Format for specifying the positions


Point Mutation(s)
Format: [ChianId]:[residue name (symbol)][residue position][residue to be mutated into(symbol)]

Example 1: To mutate Aspartic acid at position 82 in chain A to Leucine:
A:D82L

Example 2: Multiple inputs have to be separated by a comma.
A:D82L,A:H85E
Alanine Scanning
In this case the default behavior is to mutate all the residues to alanine but you can select specific residues to mutate to Alanine by unchecking the 'All positions' checkbox. After unselecting the checkbox, provide the positions to mutate as follows,

Example 1: To mutate residue at position 82 in chain A,
A:82

Example 2: You can also specify multiple residues by separating them by comma, for example to mutate residue at positions 82, 85 and 90 in chain A,
A:82,A:85,A:90
Saturation Mutagenesis
In this case the default behavior is to perform a saturation mutagenesis but you can select specific residues to mutate by unchecking the 'All positions' checkbox. After unselecting the checkbox, provide the positions to mutate as:

Example 1:To mutate residue at position 82 in chain A,
A:82

Example 2:You can also specify multiple residues by separating them by comma, for example to mutate residue at positions 82, 85 and 95 in chain A,
A:82,A:85,A:95

JOBNAME

The jobname is a name given by the user for the job. The job name is useful in distinguishing between different jobs.

Jobname is also reflected in the name of the output file created by the program.


EMAIL

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.