Mainly, 3 services are provided by the web server. They are-

1. Single Point Deletion

This service is concerned with the calculation of protein stability changes associated with single residue deletion.

2. Multi Point Deletion

This service is aimed at getting information on protein stability changes associated with multiple contiguous residue deletion.

3. Single Point Mutation

The primary goal of this service is the estimation of the effect of replacing a residue with a different residue on Protein Thermodynamic Stability

Parameters

1. Chain ID

The parameter chain id is required for making the web server aware of the chain id to work on.

2. Services

All the 3 services mentioned above have 2 modes of operation-single operation and multiple operations. A detailed explanation of the aforementioned services is provided as follows-

Single point mutation

Parameter: 1.Mutate at index -
Enter the residue position which you wish to mutate

Parameter: 2.Mutate by -
Select the amino acid from the drop down menu which you wish to mutate the above mentioned residue with..

Site specific mutagenesis

Parameter: 1.Residue start index -

Parameter: 2.Residue end index -

This calculates the stability information for all the residues From the given start index to end index. The amino acid at each position is mutated with all the other 19 Essential Amino Acids one by one and the results are calculated.

Single Point Deletion

Parameter: 1.Delete At index -
Enter the residue Position which you wish to delete

Range single point deletion

Parameter: 1.Delete start index

Parameter: 2.Delete end index

Given a start and end index, this service computes SPD for all the positions within this range.

Multi Point Deletion

Parameter: 1.Deletion From -
Enter the starting residue position to delete from

Parameter: 2.Deletion To -
Enter the Last residue postion to delete

The protein stability is calculated when all the residues from the mentioned positions are deleted. The position location values are inclusive. As an example, a range of 4 to 7 will delete residues 4,5,6,7.

Multi instance MPD

Parameter: 1.Deletion From -
Enter the starting residue position to delete from

Parameter: 2.Deletion To -
Enter the Last residue postion to delete

This service calculates the protein stability information for all possible length sequences within the given range. As an example, if deletion from = 10 and deletion to = 15 then the service runs for the following values-

Length 1: 10-11, 11-12, 12-13, 13-14, 14-15

Length 2: 10-12, 11-13, 12-14, 13-15

Length 3: 10-13, 11-14, 12-15

Length 4: 10-14, 11-15

Length 5: 10-15

4. Email Address(Optional): If the email address is provided, the result of the output is mailed to the corresponding address.

Results

Once the execution is over, the results page displays the following-

▪ PDB information

▪ Service selected and parameters provided

▪ FASTA sequence with input range highlighted

▪ Execution Result

▪ Charts or plots (for Site specific mutagenesis, Range single point deletion and Multi instance MPD)

▪ Download button (for Site specific mutagenesis, Range single point deletion and Multi instance MPD)- Downloads the charts and execution data.

▪ Tertiary structure with input range highlighted