Q. What is PEPsRNA?
PEPsRNA is a first manually curated comprehensive web resource of peptides used for siRNA delivery along with the other non-peptide conjugate molecules (like lipids etc.) All the three categories i.e. Peptide, siRNA and conjugate molecules are very well curated, documented, presented and analysed (in addition to the other experimental details).
Q. What is the need and importance of PEPsRNA database?
After discovery of the RNAi in 1998 and its potential in therapeutics, site specific delivery remains the main obstacle for its application in therapeutics. Peptides are the best answer to this problem as they are natural, small molecules compatible with natural system etc. having all the possibility of being used as carrier of siRNAs. Furthermore, the peptides have shown ability to condense the RNA molecules, cell specific delivery, endosomal escape and other properties that will be apt to be used for siRNA site specific delivery. Peptides can also be used in conjugation with lipids and other molecules for siRNA delivery.
Various siRNA based online web resources are present but none is for the delivery of the siRNAs. Therefore, there is very need for PEPsRNA like resource that will assemble all the information regarding the peptides used in delivery of the siRNAs and other associated information as we have provided here.
Q. How many total entries are there in PEPsRNA of siRNA?
PEPsRNA contains total of 2266 entries associated with experimentally tested peptide based siRNA delivery and the associated conjugate (non peptide) molecules, of which 1810 contain peptide entries and rest are used as control or siRNA only experimental testing in the studies. A total of around 280 peptides are used in reported in the database.
Additionally, we have provided the analysis of the Peptide , siRNA and information of the conjugate molecules in detail with link to external database -PubChem. Q. What are the main data fields of PEPsRNA?
The main data is divided into four categories for ease to explore as follows:-(1)Category one Peptide based information
Peptide Name(s)
Peptide Sequence(s)
Peptide Length(s)
Secondary structure with link to analysis of the peptide(s)
Click Peptide for analysis
Modification(s) in peptide
Modification Position(s)
Biological activity of peptide (2) RNA molecule based information
Linking between RNA and Peptide
Position(s) of Linking
RNA type
RNA name in paper
siRNA Sequence with link to analysis of the siRNA
siRNA length base-pair
(3) Conjugate molecule related information
Conjugate Molecule(s)
SMILES of conjugate molecules with details link
(4) General experimental information
Observation/ Target Gene
Observation percentage expression of target gene
Experiment used to check activity
siRNA concentration
Time of observation
Cell or Organism used
Title of Study
Abstract
Author (s)
Journal info (s)
Source of the study
Reference ID number.
Q. Where from will a user start the data to look in the database?
We have tried to provide the database in a sequential and easy way to be explored.
The header of the website defines the main categories in the tabs. the second tab is the "Browse" and be the first step to the user to start exploring the data. Here he can choose the various option to dig deep into the data starting with five main broad categories
(1) Peptides Sequences,
(2) Targeted Gene,
(3) Conjugate molecule,
(4) Experimental methods and
(5) Title-Reference i.e. study. On clicking any of the options, user can see the expanded list of the corresponding category. This in turn on clicking on the particular data entry will lead to the list of entries in which this particular keyword exists. Further the single data entry with all the detailed information can be explored by clicking on the data entry ID number (which is unique for each of them).
Q. How do a user search the data and how to use search option in PEPsRNA?
There are three options provided in the server to search for the data under the heading of "Search" in menu defined as follows:
(1) Basic search: This type of search uses simple terms and look into the database. Furthermore, it has two options of searching (a) Containing and (b) Exact. The former one is a kind of loose search and will look for the user defined Keyword within the database. This keyword can be anywhere in the string (words) in the database.
Exact option looks only for exact terms given by the user and will not give result if the term is not exactly provided in the data of database. (2) Advanced search: To generate the complex search with option of "AND" and "OR" e.g. Peptide "X" with conjugate "Y" (X and Y are arbitary terms). (3) Structure based search: User can draw the structure in the applet provided on the webpage and then look in the database if the structure is present or not. (Kindly, note that this applet is java based and will need the user to have updated and active java working on their system.)
Q. What are the PEPsRNA tools and what use are they of?
The PEPsRNA tools help the user to explore and analyse the user provided new data or information for similarity in the data present in the database. There are five tools that will help the user to determine the likeliness of their siRNA or peptide in the PEPsRNA, as defined below.
The five tools in PEPsRNA are: (1) Peptide Blast: To look for same or similar user provided peptide in the PEPsRNA database.(2) siRNA Blast: To look for same or similar user provided siRNA in the PEPsRNA database.(3) Map Peptide Secondary structure: To look for peptide secondary structure similarity on user provided peptide sequence.(4) siRNA Map: It looks for the siRNA from the user defined gene or longer nucleotide sequence in the database.(5) Peptide Analysis: This tool helps the user to analyse the defined peptide for various properties like composition, charge, polarity, hydrophilicity etc. Q. What and how is efficacy of peptide determined and designated in PEPsRNA web server?
There is no direct method of to determine the efficacy of the Peptide. The efficacy of a peptide is determined mainly by the indirect method of inhibition potency of associated siRNA to silence the target gene. So theoretically, if the mRNA level of silenced gene is 20% the efficacy of Peptide will be 80%. In some cases it is also mentioned via quantitative way as high or increased (as defined by the paper). Q. What is updating status of database and how user will contact to authors?
The database is updated till June 2018. Further it will be updated 6 monthly or annually or as early as the data will be available in the literature.
The users can contact the corresponding author as the link for contact and team is provided in the database.
Q. How to download data from PEPsRNA?
Data is freely available to download from PEPsRNA under the downloads section. User can download entire database in excel file format or CSV file format . Q. Is this database freely available to users have to login or give their details?
Yes, this PEPsRNA webserver is absolutely free to use for the academic and non profit research through this URL: http://bioinfo.imtech.res.in/manojk/pepsirna. The users do not have to fill any kind of information for using the data or tool in this webserver.