This page provides help to the users of CPPsite 2.0 on how to effectively use this dataset. For each module which is implemented in CPPsite 2.0, here we provide the figures and description on how to use that module. A user can click on the links given below to get help of the respective modules.
BLAST Search Blast-Search page assists users in performing BLAST search against the peptides in CPPsite 2.0. User can submit their peptide with desired BLAST options for performing similarity, server will returns the BLAST output containing list of peptides similar to the query peptide.
2-D Similarity This page provides an option to perform searching of peptides based on secondary structure states of peptides. It will help in searching peptides with similar secondary structure states to the query peptide. Users need to paste their peptide secondary structure in the textbox provided below
Smith-Waterman This page allows users to perform similarity search against peptides in CPPsite 2.0 using Smith-Waterman algorithm. User can submit their peptide; server will returns the list of peptides similar to the query peptide.
3-D Similarity This module had been designed with the aim to provide virtual screening facility to scientific community. Using this tool, users can screen their peptide library and identify similar or exact peptides from various databases. The input for this module could be provided by 1) pasting the peptide structure in defined text area OR 2) Upload the structure file in standard PDB format.
Multiple Alignment This page provides the facility to the users to align their sequence with the peptides in CPPsite 2.0. A user inputs multiple fasta sequences in the sequence box and peptide ids of CPPsite-2 in the id box, and gets aligned sequences.
Q1. What is CPPsite 2.0?
Ans .CPPsite 2.0 is updated database of cell penetrating peptides.
Q2. Why CPPsite 2.0?
Ans. It comprising peptide entries from the literature available on Pubmed and patents. It will give all the information about the cell penetrating peptide. this database will give information about the various modifications done on the CPP and the different types of cargo molecules attached to it for delivery into the cell.This database will helpfull to design novel therapeutic approach.
Q3. How to search into CPPsite 2.0?
Ans. A user can perform sequence or secondary structure-based searching to identify identical/similar entries present in all the peptide databases integrated in CPPsite 2.0.