What is AVPdb?
Antiviral Peptide Database (AVPdb) AVPdb is a manually curated, open source database of Antiviral Peptides(AVPs) targeting about 60medically important viruses.
There is no data for HIV in AVPdb. Where can I find anti- HIV peptides?
For experimentally verified anti-HIV peptides, we have developed another database, HIPdb, published in PLoS One (2013) which is freely available at http://crdd.osdd.net/servers/hipdb/
Is there any AVP prediction algorithm available?
Yes, we have developed the first antiviral prediction algorithm named AVPpred, published in NAR (2012), which successfully predicts highly effective AVPs. It is also freely available at http://crdd.osdd.net/servers/avppred/
What is the use of this database?
This database is designed keeping in mind the needs of scientific community working for antiviral therapeutics development and is hoped to be useful for research groups who are seeking a repository of AVPs. Researchers who are working on other peptides such as antimicrobial peptides, antibacterial peptides etc. can use this database to compare their peptides with those provided in AVPdb.
What are the fields in AVPdb?
1) AVPid, 2) AVP sequence, 3) AVP nomenclature, 4) AVP length, 5) Sequence, nomenclature, 6) length, 7) against virus, 8) family, source, 9) cell line, 10) inhibition(IC50/EC50/IC90/Ki/Kd/%/High/Low etc.), 11) unit, 12) target, 13) assay, 14) properties, 15) structure, 16) paper, 17) author, 18) reference and 19) accession number.
How many viruses are there in AVPdb?
There are over 60 viruses in AVPdb. These are:
Adenovirus 5, African swine fever virus, Andes virus, Avian influenza virus, Avian myeloblastosis virus, Avian sarcoma and leukosis virus- A, BK virus, Bovine herpesvirus type 1, Classical swine fever virus, Cowpox virus, Coxsackievirus, Dengue 1 virus, Dengue 2 virus, Dengue 3 virus, Dengue 4 virus, Duck hepaptitis virus, Ebola virus, Encephalomyocarditis virus, Enterovirus 71, Epstein-Barr virus, Feline immunodeficiency virus, Feline leukemia virus, Grass carp hemorrhage virus, Hendra Virus, Hepatitis B virus, Hepatitis C virus, Herpes simplex virus 1, Herpes simplex virus 2, Human cytomegalovirus, Human metapneumovirus, Human papillomavirus, Human parainfluenza virus type 2, Human parainfluenza virus type 3, Human T-cell leukaemia virus 1, Influenza A virus, Influenza B virus, Japanese encephalitis virus, Junin virus, Kaposi's sarcoma-associated herpesvirus, Lymphocytic choriomeningitis virus, Marek's disease virus, Measles virus, Mink enteritis virus, Minute virus of mice, Monkeypox virus, Murine hepatitis virus, Murine leukemia virus, Nervous necrosis nirus, Newcaslte disease virus, Newcastle disease virus, Nipah virus, Porcine reproductive and respiratory syndrome Virus, Rabies virus, Respiratory syncytial virus, SARS coronavirus, Sendai virus, Simian immunodeficiency virus, Sin nombre virus, Transmissible gastroenteritis virus, Vaccinia, West nile virus, White spot syndrome virus.
What are the tools in AVPdb?
AVPdb allows the users to take advantage of useful tools like AVPdb BLAST,AVPdb Map and peptide physicochemical properties calculator.
What does the BLAST tool do?
The 'BLAST tool' allows alignment of a given sequence against all the sequences in our database. This may help the user to confirm whether a given sequence as well as similar one has already been reported or not.
What is the use of map?
The ‘AVPdb Map’ is a user friendly tool to fetch the perfectly matching peptide available in our database. So, it helps the user to find, how many peptides against the user provided protein sequence are available in our database. The output of this tool displays the AVPid, its source, sequence, and its target. Also mentioned is the start position where the match is found in the user provided sequence.
How to use search in AVPdb?
User may perform a quick search based on AVPdb ID, Sequence, Length, Virus full name, virus abbreviation, virus family, source, cell line, target and assay. The results obtained from this search display 10 fields where first 9 contain the experimental data and the last one, Analysis, has links to BLAST results, physico-chemical properties and predicted structure of peptides.
How to use advanced search in AVPdb?
Advanced Search allows for more flexible queries based on criteria such as the viral data set of interest using logical operators (AND, OR). These options enable the user to readily identify suitable AVP related data.
How many entries are there in AVPdb?
Currently the database provides experimental information of 2059 AVPs including 624 modified AVPs.
What do you mean by modified AVPs?
Modified AVPs are those peptides which have additional chemical moieties or groups and/or non-natural amino acids attached to them apart from the natural amino acids in order to enhance their efficacy and stability. About 200 types of modifications are reported in the database.
How to view the peptide structures in Jmol?
To display the structures in your browser, make sure you have an updated version of JavaTM installed on your system and the JavaTMplugin should also be enabled in the browser.
Is this database freely available?
Yes, this open source project is freely available through this url http://crdd.osdd.net/servers/avpdb/