AVP-PEpred: Antiviral Peptide-Percent Efficacy Predictor


FAQs



Q1. What is AVP-PEpred?


AVP-PEpred is an online, open source server to predict the activity of peptides against viruses in terms of percentage inhibition values.

 

Q2. How this server is useful?


This server can be used to predict the percentage efficacy of given peptides against viruses which will then allow the experimental biologists to cut down time and cost efforts by validating a downsized set. Higher percent inhibition value may be attributable to better antiviral nature of a peptide.

 

Q3. What is the difference between already available AVP prediction algorithm (if any) and AVP-PEpred?


We had previously developed AVPpred which predicts a given peptide sequence as effective or non-effective. It is based on classification mode with SVM score as indicator of efficiency.
AVP-PEpred on the other hand is based on experimentally determined percent inhibition values taken in regression mode and thus predicts the potency of an input peptide against viruses.

 

Q4. Which machine learning techniques have been implemented in this server?


Two machine learning techniques viz. Support vector machine and Random forest have been used to design the algorithm for predicting percent inhibition values of peptides.

 

Q5. From where the data for model generation has been taken?


Experimentally determined percent inhibition values of peptides were taken from HIPdb and AVPdb. After removal of redundant sequences, 751 peptides were divided into training (601 peptides) and testing (150 peptides) datasets for evaluation.

 

Q6. Which peptide features have been for model development?

 

We have utilized important features like amino acid composition, binary and physicochemical properties etc. and their hybrids for model development.

 

Q7. Can I download the above mentioned datasets?


Yes, user can easily download the training/validation datasets. We have provided the datasets in .xls format under the “Downloads” section.

 

Q8. Are their any other tools integrated in the server?


Yes, Different tools like Mutation modules; Peptide tinker & custom mutation, Motif finder, Property calculator , BLAST, Map and Fragmenter have been incorporated in this web server. These are available under the “Tools” tab

 

Q9. What is the difference between MAP and BLAST tools?


The 'BLAST tool' performs alignment of a given sequence against all the sequences in the HIPdb and AVPdb and returns the matching sequences as per user parameters. The MAP tool is used to fetch the perfectly matching peptides available in the existing databases which map against a user provided protein sequence. It tells as to how many peptides against the user provided protein sequence have been reported earlier.

 

Q10. Is this server freely available?


Yes, the server is an open source, freely accessible server available at the url: http://crdd.osdd.net/servers/avppep.