DDGun

Untrained predictor of protein stability change upon mutation



Server Input


DDGun server has two main input interfaces. The Structure interface predicts the impact of amino acid variants on protein stability taking in input a protein structure. The Sequence interface perform the same type of prediction using only sequence information. Selecting the appropriate top button on the DDGun homepage it is possible to access both web interfaces. The two input interfaces are describes as follows:

  • Structure: Takes in input a Protein Data Bank (PDB) identifier (default option) or a PDB file provided by the user (upload button) and the chain.

  • Sequence: The sequence-based interface takes in input only the protein sequence that can be given in the textarea or uploaded in a file.

For all the input formats, the variants are provided in separated rows in the bottom textarea. Multiple mutations are represented by a comma separated format. An example of structure-based input is linked here while a sequence-based input is available here.

To prevent the submission of large processes, a maximum number of 100 variants for each job are allowed.



Server Output


After the submission of the job, DDGun server returns a link to a web page that is automatically refreshed every 20 seconds. A cgi script checks what is the status of the job in the queue system and when the job is terminate return a static html page with the predictions. In case the page is closed, the output of your job can be retrieved using the JobID and the form in the Job web page Depending from the input format, DDGun displays different information.
When running in structure mode for each variant the prediction row includes the following data: the pdbfile, the chain, the mutation, four scores calculated by the method (Kyte-Dolittle, Blosum62, Skolnick and Bastolla) the relative solvent accessible area of the wild-type and mutant residues, and predicted ΔΔGu. For each row a green button opens a window where more information about the variant are reported. The the displayed data includes the variation of the Kyte-Dolittle Hydropathy Index, the frequency of wild-type and mutant residues in the multiple sequence alignment, the structural environment of the mutated residue, and the predicted ΔΔGu for the single mutant. In particular when the method predicts the effect of multiple site variants the information calculated for each single variant are reported in separated rows. An example of the output table is reported below.



When DDGun is running in sequence mode the server output reports only sequence-based information which includes: the mutation, three scores calculated by the method (Kyte-Dolittle, Blosum62, and Skolnick) and predicted ΔΔGu. Similarly to the structure-based prediction, a green button allow to diply more detail for the predictons including the variation of the Kyte-Dolittle Hydropathy Index, the frequency of wild-type and mutant residues in the multiple sequence alignment and the predicted ΔΔGu for the single mutant. An example of the output table is reported below.



Parsable Textfile Output


The parsable textfile output of the server includes many of the data reported in the webpage In detail the DDGun textfile output contains the following information.



	In Structure-based mode DDGun returns in output:

	PDBFILE: PDB file name
	CHAIN: PDB chain
	VARIANT: Protein mutation
	CONSERVATION: Frequencies of the wild-type and mutant residues in the mutated positions.
	CONTACTS: List of residues within 5.0 Ang from the mutated positions.
	S_KD: Kyte-Doolittle substitution scores (AAINDEX1:KYTJ820101).
	S_BL: BLOSUM62 substitution score (AAINDEX2:HENS920102).
	S_PROF: Profile-based scores based on Skolnick potential (AAINDEX3:SKOJ970101).
	S_3D: Structural environment score for the wild-type protein based on Bastolla potential (AAINDEX3:BASU010101).
	RSA: Relative Solvent Accessible area for the wild-type residues.
	DDG: Prediction of the DDG for the single amino acid substitutions
	T_DDG: Global DDG for multiple amino acid substitutions

        An example of output is linked here.


	In Sequence-based mode DDGun returns in output:

	SEQFILE: Sequence file name.
	VARIANT: Protein mutation.
	CONSERVATION: Frequencies of the wild-type and mutant residues in the mutated positions.
	S_KD: Kyte-Doolittle substitution scores (AAINDEX1:KYTJ820101).
	S_BL: BLOSUM62 substitution score (AAINDEX2:ENS920102).
	DDG: Prediction of the DDG for the single amino acid substitutions.
	T_DDG: Global DDG for multiple amino acid substitutions.

	An example of output is linked here.