Tag: Peptide

PeptideReranking – Peptide Re-ranking with Protein-peptide Correspondence and Precursor Peak Intensity Information

PeptideReranking

:: DESCRIPTION

PeptideReranking includes three peptide reranking methods: PPMRanker, PPIRanker, and MIRanker. PPMRanker only uses Protein-Peptide Map (PPM) information from the protein database, PPIRanker only uses Precursor Peak Intensity (PPI) information, and MIRanker employs both PPM information and PPI information.

::DEVELOPER

Laboratory for Bioinformatics and Computational Biology, HKUST

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PeptideReranking

:: MORE INFORMATION

Citation:

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jul-Aug;9(4):1212-9. doi: 10.1109/TCBB.2012.29.
Peptide reranking with protein-peptide correspondence and precursor peak intensity information.
Yang C1, He Z, Yang C, Yu W.

MUSI – MUltiple Specificity Identifier

MUSI

:: DESCRIPTION

MUSI is a tool for uncovering multiple peptides and nucleic acids binding specificities from sequence data. MUSI provides a simple interface for processing short peptides or nucleic acid sequence data. Starting from a set of sequences observed to bind to a given target, it automatically generates an optimal number of motifs based on the different specificity patterns present in the data.

::DEVELOPER

Kim Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 MUSI

:: MORE INFORMATION

Citation

MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets.
Kim T, Tyndel MS, Huang H, Sidhu SS, Bader GD, Gfeller D, Kim PM.
Nucleic Acids Res. 2012 Mar;40(6):e47. doi: 10.1093/nar/gkr1294

POW – PDZ Domain-peptide Interaction Prediction

POW

:: DESCRIPTION

POW is a website that allows users to predict PDZ domain-peptide interactions for human, mouse, worm and fly PDZ domains.

::DEVELOPER

Bader Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Jan 21;14:27. doi: 10.1186/1471-2105-14-27.
Predicting PDZ domain mediated protein interactions from structure.
Hui S1, Xing X, Bader GD.

iATP – Identifying Anti-tubercular Peptides

iATP

:: DESCRIPTION

The web-server iATP was developed to identify the anti-tubercular peptides based on the sequence information.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iATP: A sequence based method for identifying anti-tubercular peptides
Chen W, Feng P, Nie F.
Med Chem. 2019 Oct 2. doi: 10.2174/1573406415666191002152441.

iACP – A sequence-based tool for Identifying Anticancer Peptides

iACP

:: DESCRIPTION

The web-server iACP was developed to identify the anticancer peptides based on the sequence information.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iACP: a sequence-based tool for identifying anticancer peptides.
Chen W, Ding H, Feng P, Lin H, Chou KC.
Oncotarget. 2016 Mar 1. doi: 10.18632/oncotarget.7815.

IL4pred – Designing and Disovering of Interleukin-4 inducing peptides

IL4pred

:: DESCRIPTION

IL4pred web server is developed for users working in the field of vaccine design. This server allows users to predict and design Interleukin-4 (IL4) inducing peptides.

::DEVELOPER

IL4pred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Prediction of IL4 inducing peptides.
Dhanda SK, Gupta S, Vir P, Raghava GP.
Clin Dev Immunol. 2013;2013:263952. doi: 10.1155/2013/263952.

HLP – Predicting Half-life of Peptides in Intestine like Environment

HLP

:: DESCRIPTION

HLP is a server developed for predicting half-life of peptides in intestine like environment. It generates all possible mutants (single mutation at each position per cycle) for a peptide and predict/calculate half-life and physicochemical properties (e.g. charge, polarity, hydrophobicity, volume, pK) of mutant peptides.

::DEVELOPER

HLP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Designing of peptides with desired half-life in intestine-like environment.
Sharma A, Singla D, Rashid M, Raghava GP.
BMC Bioinformatics. 2014 Aug 20;15:282. doi: 10.1186/1471-2105-15-282.

AHTpin – Predicting, Designing and Screening of AHT Peptides

AHTpin

:: DESCRIPTION

AHTpin is an in silico method developed to predict and design efficient antihypertensive peptides.

::DEVELOPER

AHTpin team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

An in silico platform for predicting, screening and designing of antihypertensive peptides.
Kumar R, Chaudhary K, Singh Chauhan J, Nagpal G, Kumar R, Sharma M, Raghava GP.
Sci Rep. 2015 Jul 27;5:12512. doi: 10.1038/srep12512.

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

 NO

:: 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.

PlifePred – Design Half-life of Peptides in Blood

PlifePred

:: DESCRIPTION

PlifePred is prediction server for predicting the half-life of peptides in blood. Users can use PlifePred to increase or decrease the half-life of their peptide by generating mutants. The server facilitates designing the half-life of a peptide by generating its mutants and predicting their half-life and physiochemical properties.The user can screen and select the peptide with suitable properties desired.

::DEVELOPER

PlifePred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

In silico approaches for predicting the half-life of natural and modified peptides in blood.
Mathur D, Singh S, Mehta A, Agrawal P, Raghava GPS.
PLoS One. 2018 Jun 1;13(6):e0196829. doi: 10.1371/journal.pone.0196829.