PDEXK – Server for Detection of new Protein Families from the PD-(D/E)XK Superfamily

PDEXK

:: DESCRIPTION

The PDEXK server is developed for detecting new protein families of the PD-(D/E)XK superfamily using Support Vector Machines trained on data derived from profile-profile alignments. Using a number of both superfamily-specific and general features, SVMs were trained to identify true positive alignments of PD-(D/E)XK representatives.

::DEVELOPER

VU Institute of Biotechnology

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Laganeckas M., Margelevičius M., Venclovas Č. (2010)
Identification of new homologs of PD-(D/E)XK nucleases by Support Vector Machines trained on data derived from profile-profile alignments.
Nucl. Acids Res. (2011) 39 (4): 1187-1196.

partiFold – Transmembrane Beta-barrel Proteins Predictor

partiFold / partiFold-Align

:: DESCRIPTION

partiFold is a software to investigate the folding landscape of TMBs (Transmembrane Beta-barrel Proteins).

partiFold-Align is the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm’s complexity is polynomial in time and space.

::DEVELOPER

Jerome Waldispühl , Bonnie Berger

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX
  • WebServer

:: DOWNLOAD

 partiFold

:: MORE INFORMATION

Citation:

Simultaneous alignment and folding of protein sequences.
Waldispühl J, O’Donnell CW, Will S, Devadas S, Backofen R, Berger B.
J Comput Biol. 2014 Jul;21(7):477-91. doi: 10.1089/cmb.2013.0163

J. Waldispühl, C.W. O’Donnell, S. Devadas, P. Clote and B. Berger.
Modeling Ensembles of Transmembrane β-barrel Proteins
PROTEINS: Structure, Function and Bioinformatics, published online 14 Nov. 2007. doi:10.1002/prot.21788

NIAS-Server 1.0 – Neighbors Influence of Amino acids and Secondary Structures in Proteins

NIAS-Server 1.0

:: DESCRIPTION

NIAS is a server to help the analysis of the conformational preferences of amino acid residues in proteins.

::DEVELOPER

SBCB – Structural Bioinformatics and Computational Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

NIAS-Server: Neighbors Influence of Amino acids and Secondary Structures in Proteins.
Borguesan B, Inostroza-Ponta M, Dorn M.
J Comput Biol. 2016 Aug 5.

TepiTool – Computational Prediction of T Cell Epitope Candidates

TepiTool

:: DESCRIPTION

The Tepitool provides prediction of peptides binding to MHC class I and class II molecules.

::DEVELOPER

the IEDB Solutions Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TepiTool

:: MORE INFORMATION

Citation

TepiTool: A Pipeline for Computational Prediction of T Cell Epitope Candidates.
Paul S, Sidney J, Sette A, Peters B.
Curr Protoc Immunol. 2016 Aug 1;114:18.19.1-18.19.24. doi: 10.1002/cpim.12.

MetaPred2CS 1.1 – Meta-predictor for Protein-protein Interactions of Prokaryotic Two-component System Proteins

MetaPred2CS 1.1

:: DESCRIPTION

MetaPred2CS Web server is a meta-predictor based on Support Vector Machine (SVM) that combines 6 individual sequence based protein-protein interaction prediction methods to predict prokaryotic two-component system protein-protein interactions (PPIs).

::DEVELOPER

Bioinformatics @ IBERS

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MetaPred2CS

:: MORE INFORMATION

Citation

Bioinformatics. 2016 Jul 4. pii: btw403.
MetaPred2CS: a sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteins.
Kara A, Vickers M, Swain M, Whitworth DE, Fernandez-Fuentes N.

EPISOFT – Epitope Vaccine Optimization Server

EPISOFT

:: DESCRIPTION

EPISOFT predicts epitope HLA I binding profiles and computes population protection (PPC). It also identifies minimal sets of epitopes that reach a target PPC for 5 distinct user-selected ethnic groups.

::DEVELOPER

Immunomedicine Group 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

Towards the Knowledge-based Design of Universal Influenza Epitope Ensemble Vaccines.
Sheikh QM, Gatherer D, Reche PA, Flower DR.
Bioinformatics. 2016 Jul 10. pii: btw399.

MP3 1.0 – Prediction of Pathogenic Proteins in Metagenomic and Genomic Datasets

MP3 1.0

:: DESCRIPTION

MP3 is a standalone tool and web server for the prediction of pathogenic proteins in both genomic and metagenomic datasets.

::DEVELOPER

MetaBioSys laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MP3

:: MORE INFORMATION

Citation

MP3: a software tool for the prediction of pathogenic proteins in genomic and metagenomic data.
Gupta A, Kapil R, Dhakan DB, Sharma VK.
PLoS One. 2014 Apr 15;9(4):e93907. doi: 10.1371/journal.pone.0093907.

ProInflam – Prediction of Proinflamatory Epitopes

ProInflam

:: DESCRIPTION

ProInflam is a webserver for the prediction of proinflammatory antigenicity of peptides and proteins.

::DEVELOPER

MetaBioSys laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ProInflam: a webserver for the prediction of proinflammatory antigenicity of peptides and proteins.
Gupta S, Madhu MK, Sharma AK, Sharma VK.
J Transl Med. 2016 Jun 14;14(1):178. doi: 10.1186/s12967-016-0928-3.

HyPe – A Peptidoglycan Hydrolase Prediction Tool

HyPe

:: DESCRIPTION

HyPe helps in the identification and classification of novel peptidoglycan hydrolases from complete genomic or metagenomic ORFs.

::DEVELOPER

MetaBioSys laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HyPe

:: MORE INFORMATION

Citation

Prediction of peptidoglycan hydrolases- a new class of antibacterial proteins.
Sharma AK, Kumar S, K H, Dhakan DB, Sharma VK.
BMC Genomics. 2016 May 27;17(1):411. doi: 10.1186/s12864-016-2753-8.

DAPPLE 2 – Homology-based Prediction of Phosphorylation Sites

DAPPLE 2

:: DESCRIPTION

DAPPLE is a homology-based method for predicting phosphorylation sites in an organism of interest. It uses BLAST searches of experimentally-determined phosphorylation sites in one organism (or several organisms) to predict phosphorylation sites in an organism of interest. It outputs a table containing information helpful for choosing phosphorylation sites that are of interest to you, such as the number of sequence differences between the query site and the hit site, the location of the query site and the hit site in their respective intact proteins, and whether the corresponding intact proteins are reciprocal BLAST hits (and thus predicted orthologues).

::DEVELOPER

Bioinformatics Research Group, University of Saskatchewan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

DAPPLE 2: a tool for the homology-based prediction of post-translational modification sites.
Trost B, Maleki F, Kusalik A, Napper S.
J Proteome Res. 2016 Jul 1.

Bioinformatics. 2013 Jul 1;29(13):1693-5. doi: 10.1093/bioinformatics/btt265. Epub 2013 May 8.
DAPPLE: a pipeline for the homology-based prediction of phosphorylation sites.
Trost B, Arsenault R, Griebel P, Napper S, Kusalik A.