PEPlife – Database of Half-life of Peptides

PEPlife

:: DESCRIPTION

PEPlife is a manually curated database of experimentally validated therapeutic peptides and their halflives. In this database, peptides have been collected from both published articles as well as from patents.Each entry provides comprehensive information about a peptide that includes its sequence, chemical modifications incorporated, biological activity possessed, its half-life, the assay used to determine its half-life etc.

::DEVELOPER

PEPlife team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

PEPlife: A Repository of the Half-life of Peptides.
Mathur D, Prakash S, Anand P, Kaur H, Agrawal P, Mehta A, Kumar R, Singh S, Raghava GP.
Sci Rep. 2016 Nov 7;6:36617. doi: 10.1038/srep36617.

CancerPDF – Cancer Peptidome Database of BioFluids

CancerPDF

:: DESCRIPTION

CancerPDF is a manually curated database of cancer-associated peptides found in different human bodyfluids (e.g., serum, urine, plasma and saliva). These peptides were experimentally identified using diffrent techniques of proteomics. It covers nearly 30 types of human cancers.

::DEVELOPER

CancerPDF team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

CancerPDF: A repository of cancer-associated peptidome found in human biofluids.
Bhalla S, Verma R, Kaur H, Kumar R, Usmani SS, Sharma S, Raghava GPS.
Sci Rep. 2017 May 4;7(1):1511. doi: 10.1038/s41598-017-01633-3.

THPdb – Database of FDA approved Therapeutic Peptides and Proteins

THPdb

:: DESCRIPTION

THPdb is a manually curated repository of Food and Drug Administration (FDA) approved therapeutic peptides and proteins

::DEVELOPER

THPdb team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser / Android

:: DOWNLOAD

THPdb

:: MORE INFORMATION

Citation

THPdb: Database of FDA-approved peptide and protein therapeutics.
Usmani SS, Bedi G, Samuel JS, Singh S, Kalra S, Kumar P, Ahuja AA, Sharma M, Gautam A, Raghava GPS.
PLoS One. 2017 Jul 31;12(7):e0181748. doi: 10.1371/journal.pone.0181748.

TopicalPdb – Database of Topically Administered Peptide

TopicalPdb

:: DESCRIPTION

TopicalPdb contains 657 peptide entries alongwith their secondary & tertiary structure. This database maintains experimentally validated peptides that are topically and non-invasively administered via transdermal, occular and nasal routes.

::DEVELOPER

TopicalPdb team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

TopicalPdb: A database of topically delivered peptides.
Mathur D, Mehta A, Firmal P, Bedi G, Sood C, Gautam A, Raghava GPS.
PLoS One. 2018 Feb 12;13(2):e0190134. doi: 10.1371/journal.pone.0190134.

AntiTbPdb – Anti-Tubercular Peptide Database

AntiTbPdb

:: DESCRIPTION

AntiTbPdb is a database of experimentally verified anti-tubercular or anti-mycobacterial peptides. AntiTbPdb contains around 1010 entries extracted from research papers and patents. It provides detail information of each peptide such as sequence, modifications, nature, source or origin of the peptide, strain-specific mycobacterium species, inhibition concentration of peptides, its specific immune response, etc. Beside this, it also contains possible predicted structures of these anti-tubercular peptides.

::DEVELOPER

AntiTbPdb team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

AntiTbPdb: a knowledgebase of anti-tubercular peptides.
Usmani SS, Kumar R, Kumar V, Singh S, Raghava GPS.
Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay025.

HumCFS – A Database Of Human Chromosomal Fragile Sites

HumCFS

:: DESCRIPTION

HumCFS is a manually curated database of human chromosomal fragile sites. HumCFS provides useful information about 125 human chromosomal fragile sites and their association with 4921 human protein-coding genes and 917 human miRNA’s.

::DEVELOPER

HumCFS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

HumCFS: a database of fragile sites in human chromosomes.
Kumar R, Nagpal G, Kumar V, Usmani SS, Agrawal P, Raghava GPS.
BMC Genomics. 2019 Apr 18;19(Suppl 9):985. doi: 10.1186/s12864-018-5330-5.

PRRDB 2.0 – Pattern Recognition Receptor Database

PRRDB 2.0

:: DESCRIPTION

PRRDB is a comprehensive database of pattern recognition receptors and their ligands. This is an updated version of the database PRRDB. It contains extensive information about 467 unique pattern-recognition receptors and 827 ligands manually extracted from ~600 research articles.

::DEVELOPER

PRRDB team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

PRRDB 2.0: a comprehensive database of pattern-recognition receptors and their ligands.
Kaur D, Patiyal S, Sharma N, Usmani SS, Raghava GPS.
Database (Oxford). 2019 Jan 1;2019. pii: baz076. doi: 10.1093/database/baz076.

MHCBN 4.0 – Database of MHC/TAP Binding Peptides and T-cell Epitopes

MHCBN 4.0

:: DESCRIPTION

The MHCBN is a curated database consisting of detailed information about Major Histocompatibility Complex (MHC) Binding,Non-binding peptides and T-cell epitopes.The version 4.0 of database provides information about peptides interacting with TAP and MHC linked autoimmune diseases.

::DEVELOPER

MHCBN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

MHCBN 4.0: A database of MHC/TAP binding peptides and T-cell epitopes.
Lata S, Bhasin M, Raghava GP.
BMC Res Notes. 2009 Apr 20;2:61. doi: 10.1186/1756-0500-2-61.

PCMdb – Pancreatic Cancer Methylation Database

PCMdb

:: DESCRIPTION

PCMdb is a database of methylated genes found in pancreatic cancer cell lines and tissues. In other words, it provides comprehensive information about methylation status of various genes in Pancreatic Cancer (PCa) and their comparison with transcriptomics and genomics landscape. It is a manually curated database where information is collected and compiled from literature/databases. This database will be very useful to discover novel biomakers for PCa as well as to understand the role of methylation in drug resistance.

::DEVELOPER

PCMdb team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

PCMdb: pancreatic cancer methylation database.
Nagpal G, Sharma M, Kumar S, Chaudhary K, Gupta S, Gautam A, Raghava GP.
Sci Rep. 2014 Feb 26;4:4197. doi: 10.1038/srep04197.

M-Coffee – Combination of Multiple Sequence Alignment Packages

M-Coffee

:: DESCRIPTION

M-Coffee is a multiple sequence alignment Package. It is part of the T-Coffee distribution. The specificity of M-Coffee is that rather than computing a multiple sequence alignment on its own, it uses other packages to compute the alignments. It then uses T-Coffee to combine all these alignents into one unique final alignment.

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

M-Coffee: combining multiple sequence alignment methods with T-Coffee.
Wallace IM, O’Sullivan O, Higgins DG, Notredame C.
Nucleic Acids Res. 2006 Mar 23;34(6):1692-9. Print 2006.

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.
Moretti S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W645-8. Epub 2007 May 25.