Predicting the functional consequences of point mutations in proteins.

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Since 'Alanine Scanning' is not to be performed over all the residues, please provide the positions at which 'Alanine' mutants are to be tested.
For more details you can also refer to Format help and examples page.
Since 'Saturation Mutagenesis' is not to be performed over all the residues, please provide the positions at which mutants are to be tested.
For more details you can also refer to Format help and examples page.
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Point Mutation(s)

Alanine Scanning

Saturation Mutagenesis

All positions



Optional parameters

 
 
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Parameters with help content are in bold face.

PDB Structure
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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.

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MUTATIONS

There are three ways to specify the mutation(s):

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 this option is selected then the user has the choice of either mutating all the positions to 'Alanine' (this is also the default choice). Also, the user can specify the 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 this 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
Format:[ChianId]:[residue position]

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
Format: [ChianId]:[residue position]

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

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