Prediction of peptide antiviral activity in terms of IC50
FAQs
Q1. What is AVP-IC50Pred?
AVP-IC50Pred is an online, open source server to predict the numerical efficacy of antiviral peptides in terms of their IC50 values.
Q2. What is the use of AVP-IC50Pred?
This server can be used to predict the antiviral potential of given peptides which will then enable the researchers to validate a concentrated set experimentally, thus reducing time and efforts. This server predicts the IC50 values in μM units. Hence, lower the IC50 value better is the antiviral nature of a peptide.
Q3. Is there any other AVP prediction algorithm present previously? If yes, then what is the difference between them and AVPIC50pred?
Yes, we have previously developed AVPpred in the past 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-IC50Pred on the other hand is based on experimentally determined IC50 values (μM) taken in regression mode and thus predicts the IC50 value of an input peptide in these units.
Q4. Which machine learning techniques have been implemented in this server?
Four different machine learning techniques have been used to design the algorithm for predicting IC50 values of peptides. These include Support Vector Machine, Random Forest, IBk and K-Star. These techniques have been briefed in the “Algorithm” section of this server.
Q5. What type of data was used to generate the models for prediction?
Peptides having quantitative IC50 values were selected from HIPdb and AVPdb. After removal of redundant sequences, there were left 759 peptides, which were divided into training (683 peptides) and testing (76 peptides) datasets for evaluation.
Q6. What features were used during model development?
We have utilized important features like amino acid composition, binary and physicochemical properties etc. 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 .csv format under the “Downloads” section.
Q8. What are the other tools provided in the server?
Additional tools like AVP-IC50 Conserve, BLAST, Map, Peptide generator, Peptide physicochemical properties calculator and motif scan have been incorporated in this web server. These are available under the “Tools” tab
Q9. What is Mutation analyzer?
Mutation analyzer is a tool available under “AVP-IC50mut” tab which generates all possible mutants of a given peptide and further predicts their antiviral activity in terms of IC50. We have carried out the prediction and analysis of IC50 of all single mutants of the AVPs in our dataset. This has been provided under the same tab.
Q10. How does AVP-IC50 Conserve works?
AVP-IC50 Conserve works by checking the conservation of user provided peptide sequence in human, viral and antiviral proteins. The output of this tool is presented in a tabular form with columns showing uniprot accession no, organism name against which the peptide sequence has been found to be conserved, protein name, start position, alignment, end position and percent identity.
Q12. What is Motif scan tool and how is it useful?
Motif scan allows to search possible AVP motifs in user provided protein/peptide sequences. This tool is based on MEME/MAST software which helps in aligning the motifs found in the user sequence with those present in AVPs to classify the motif unser consideration as AVP motif or not.
Q13. 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.
Q14. Is this server freely available?
Yes, the server is an open source, freely accessible server available at the url: http://crdd.osdd.net/servers/ic50avp.