An algorithm for prediction of highly effective AVPs based on experimentally validated positive and negative data sets. AVPpred contains four prediction models : the composition-based, physico-chemical properties and sequence alignment-based were implemented in the web server to make comprehensive predictions. AVPpred would be helpful for researchers working for the development of peptide-based antiviral therapeutics.
Detects highly specific and selective peptides. PHASTpep can be applied from simple purified protein screens to more complex in vitro cell, in vivo, or ex vivo tissue screening. This method allows the importation of sequences, pulls out the portion of DNA corresponding to the displayed peptides, translates the sequences into amino acids, and calculates the frequency of each unique peptide.
A web server for prediction and design of antiviral compounds. AVCpred web server includes the following modules: (i) Submissions (allows users to submit on or more molecules at a time), (ii) Design analogs (user can design analogs based on given building blocks and predict their inhibition on the viruses), (iii) Draw structure (can sketch the structure of the query molecule using Marvin editor), and (iv) Search (provides the users a search tool to browse the compounds used in our datasets. In this module, different compounds targeting the viruses are stored in a database).
Predicts fusion peptide domain of retroviruses, including HERV, HIV, SIV, HTLV and MLV. Fptool is a sequence-based FP model combining Hidden Markov Method with similarity comparison. FP model predicts np-FP domain through two phases. Firstly, it adopted HMM method to determine the existence and rough location of np-FP. Subsequently, it performed similarity comparison for a more precise np-FP.
Predicts the antiviral activity in terms of IC50 values (µM). AVP-IC50Pred is a regression-based algorithm that permits generation of all possible combinations of amino acid mutations in a given peptide sequence and prediction of the IC50 of the mutant peptides. It also enables users to sort the mutant peptides as per their predicted IC50 value to select the highly effective peptides. This software aims to assist researchers working on antiviral peptide (AVP) therapeutics.