Tag: Specificity

PROSPER – Protease Substrate Specificity Webserver

PROSPER

 

:: DESCRIPTION

PROSPER (PROtease substrate SPecificity servER) is an integrated feature-based webserver for in silico prediction of protease substrates and their cleavage sites for twenty-four different protease types, covering four major protease families- Aspartic (A), Cysteine (C), Metallo (M) and Serine (S).

::DEVELOPER

Whisstock Laboratory,  Monash University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Web Server
  • Perl

:: DOWNLOAD

 PROSPER

:: MORE INFORMATION

Citation:

PLoS One. 2012;7(11):e50300. doi: 10.1371/journal.pone.0050300.
PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites.
Song J, Tan H, Perry AJ, Akutsu T, Webb GI, Whisstock JC, Pike RN.

HRSS 0.2 – Hybrid Relative Specificity Similarity based on Gene Ontology

HRSS 0.2

:: DESCRIPTION

HRSS provides a hybrid GO-based semantic similarity algorithm for evaluating the functional similarity between GO terms or gene products.

:: DEVELOPER

Center for Plant Environmental Sensing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MySQL

:: DOWNLOAD

 HRSS

:: MORE INFORMATION

Citation

Wu, X., Pang, E., Lin, K. and Pei, Z.M. (2013)
Improving the Measurement of Semantic Similarity between Gene Ontology Terms and Gene Products: Insights from an Edge- and IC-Based Hybrid Method.
PLoS One 8(5), e66745. doi:10.1371/journal.pone.0066745

SPEER 201010 – Prediction of Protein Specificity Determining Sites

SPEER 201010

:: DESCRIPTION

‘SPEER-SERVER‘ (Specificity prediction using amino acids’ Properties, Entropy and Evolution Rate) is a web server that encodes the specific conservation pattern of amino acid types in a protein family to identify the specificity determining sites (SDS). The specific conservation pattern is predicted using amino acids’ physico-chemical properties, relative entropy and the evolutionary rates between the protein subfamilies.

::DEVELOPER

SPEER team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

  SPEER

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W242-8. doi: 10.1093/nar/gks559. Epub 2012 Jun 11.
SPEER-SERVER: a web server for prediction of protein specificity determining sites.
Chakraborty A, Mandloi S, Lanczycki CJ, Panchenko AR, Chakrabarti S.

TrSSP – Transporter Substrate Specificity Prediction Server

TrSSP

:: DESCRIPTION

TrSSP is an integrative Support Vector Machine (SVM) based transporter substrate specificity predictor that is based on primary sequence information such as amino acid composition, AAIndex composition and PSSM profiles.

::DEVELOPER

The Zhao Bioinformatics Laboratory

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Prediction of membrane transport proteins and their substrate specificities using primary sequence information.
Mishra NK, Chang J, Zhao PX.
PLoS One. 2014 Jun 26;9(6):e100278. doi: 10.1371/journal.pone.0100278

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

PreMoTF 20121109 – Homeodomain Specificity Predictions

PreMoTF 20121109

:: DESCRIPTION

PreMoTF  (Predicted Motifs for Transcription Factors) predicts PFMs (position frequency matrices) for homeodomain proteins based on protein sequence

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jun 15;28(12):i84-9. doi: 10.1093/bioinformatics/bts202.
Recognition models to predict DNA-binding specificities of homeodomain proteins.
Christensen RG1, Enuameh MS, Noyes MB, Brodsky MH, Wolfe SA, Stormo GD.

NRPSpredictor2 20111113 – Predict NRPS Adenylation Domain Specificity

NRPSpredictor2 20111113

:: DESCRIPTION

NRPSpredictor, based on Transductive Support Vector Machines (TSVMs) was built on these 34 active site residues to predict A-domain specificity. The products of many bacterial non-ribosomal peptide synthetases (NRPS) are highly important secondary metabolites, including vancomycin and other antibiotics. The ability to predict substrate specificity of newly detected NRPS Adenylation (A-) domains by genome sequencing efforts is of great importance to identify and annotate new gene clusters that produce secondary metabolites. Prediction of A-domain specificity based on the sequence alone can be achieved through sequence signatures or, more accurately, through machine learning methods.

::DEVELOPER

APPLIED BIOINFORMATICS GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 NRPSpredictor2

:: MORE INFORMATION

Citation

Röttig et al.
NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity
Nucleic Acids Research 39 (suppl 2): W362-W367 (2011)

Predikin – Predict Substrate Specificity of Protein Kinases

Predikin

:: DESCRIPTION

Predikin is a system to predict substrate specificity of protein kinases.

::DEVELOPER

Kobe Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

   NO

:: MORE INFORMATION

Citation

The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information.
Saunders NF, Kobe B.
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W286-90. doi: 10.1093/nar/gkn279

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