dPABBs: A webserver for Designing of Peptides Against Bacterial Biofilms
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dPABBs Help

dPABBs is a user friendly webserver where user can submit their query as peptide, protein and multiple peptide sequences (in batch mode). Detailed information about each module is given below:

Peptide
There user can predict the anti-biofilm ability of the submitted peptide on the basis of SVM / Weka based prediction method. The mutants of the originally submitted peptide are generated.



Stepwise description of Peptide module is given below
  1. Input sequence:- User can paste the peptide sequence directly into the input box. Sequences must be entered in the single letter code. All the non-natural amino acids and characters will be ignored from the peptide sequence.
  2. User can select from the different SVM / Weka based models for predicting the anti-biofilm activity of peptides at particular threshold( range -1 to +1) provided for user.
  3. All possible mutants (containing anti-biofilm ability in the form of SVM score / Weka probability and user selected physicochemical properties) for user submitted peptide will be generated.
  4. Original peptide and its mutants are shown in tabular form. The red colored residue in mutants depicts the substituted residue.
  5. The results can be sorted in ascending as well as descending order of their values. This will help to identify best putative anti-biofilm peptide (i.e., with highest SVM score / Weka probability) from the list of peptides.
  6. Best putative anti-biofilm peptide can further be used to generate all possible mutants to get still more anti-biofilm peptides.


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Protein
There user can identify anti-biofilm regions from the protein of interest. Possible peptides are generated from the protein using overlapping window concept. The snapshot given below gives a very brief idea about this module.


The results from Protein module may be generated in following two modes:

Tabular Mode
The brief description is given below:
  1. Paste the protein (in single letter code, single line sequence only) in the input box. After submission, all possible peptides are generated containing putative anti-biofilm ability (in the form of SVM score / Weka probability) with physicochemical properties.
  2. Results are displayed in tabular form (having desired physicochemical properties choosen by the user).
  3. Mutants of the fragments with anti-biofilm properties can be generated further by just clicking on the fragment. The later will help to generate best putative anti-biofilm peptides.

Graphic Mode
The results are displayed in two patterns, one showing the whole protein (in terms of all overlapping peptide fragments) prediction results (SVM score / Weka probability) accompanied with four physicochemical properties (i.e., Hydrophobicity, Hydrophilicity, Charge, Molecular weight). Clicking upon a particular physicochemical property e.g., on the basis of SVM score (at a particular threshold), no. of peaks will decide possible anti-biofilm peptides present in protein sequence.
The other pattern is displayed for fragments which are generated from the submitted protein. The predicted bioactivity value (SVM score / Weka probability) accompanied with physicochemical properties (Hydrophobicity, Hydrophilicity, Charge, Molecular weight) and the peptide fragments for that protein are displayed. On clicking the peptide fragments, the predicted bioactivity scores / properties are displayed in graphical form.



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Batch
Through this module, user can submit more than one peptide sequence (either by pasting the peptide sequences in text box or uploading the file containing peptide sequences) in FASTA format only. Thus, it will be helpful in high-throughput screening of peptides. Further, all the possible mutants may be generated for the original peptide (just clicking on it).




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MultiModel
Through this module, user can select multiple models to predict anti-biofilm activity for more than one peptide sequence (either by pasting the peptide sequences in text box or uploading the file containing peptide sequences) in FASTA format only. Thus, it will be helpful in high-throughput screening of peptides. Further, all the possible mutants may be generated for the original peptide (refer to screenshot given below).




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Citation: If you are using this server, please cite:

Gupta, P. et al. dPABBs: A Novel in silico Approach for Predicting and Designing Anti-biofilm Peptides. Sci. Rep. 6, 21839; doi: 10.1038/srep21839 (2016).



Developed by: OSDD Unit, CSIR- HQ, New Delhi- 110001