Tag: Disorder

MobiDB-lite 3.8.4 – Long Disorder Consensus Predictor

MobiDB-lite 3.8.4

:: DESCRIPTION

MobiDB-lite is an optimized method for highly specific predictions of long intrinsically disordered regions (IDRs). The method uses 8 different predictors to derive a consensus which is filtered for spurious short predictions in a second step.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

MobiDB-lite

:: MORE INFORMATION

Citation:

Necci M, Piovesan D, Clementel D, Dosztányi Z, Tosatto SCE.
MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavours in proteins.
Bioinformatics. 2020 Dec 16:btaa1045. doi: 10.1093/bioinformatics/btaa1045. Epub ahead of print. PMID: 33325498.

PON-Diso – Protein Disorder Prediction

PON-Diso

:: DESCRIPTION

PON-Diso is a machine learning based prediction method, which is developed using Random Forest classifier on AAIndex features and Evolutionary features. PON-Diso is a method to predict changes in disorder regions contained in protein caused by amino acid substitutions.

::DEVELOPER

Protein Structure and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Hum Mutat. 2014 Jul;35(7):794-804. doi: 10.1002/humu.22564. Epub 2014 May 21.
Performance of protein disorder prediction programs on amino acid substitutions.
Ali H1, Urolagin S, Gurarslan Ö, Vihinen M.

DISOPRED 3.16 – Intrinsic Protein Disorder Prediction

DISOPRED 3.16

:: DESCRIPTION

DISOPRED is a SVM-based predictor of disordered regions in proteins.

:DEVELOPER

Bioinformatics Group – University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/Unix/MacOsX
  • any ANSI C and C++ compiler

:: DOWNLOAD

 DISOPRED

:: MORE INFORMATION

Citation

Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF and Jones DT (2004)
Prediction and functional analysis of native disorder in proteins from the three kingdoms of life.
J. Mol. Biol., 337, 635-645.

SoftPanel – Grouping Disorders for Generation of customized Panels

SoftPanel

:: DESCRIPTION

SoftPanel provides a convenient and powerful tool for creating a targeted panel of potential disease genes while supporting different forms of input.

::DEVELOPER

SoftPanel team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 SoftPanel

:: MORE INFORMATION

Citation

SoftPanel: a website for grouping diseases and related disorders for generation of customized panels.
Wang L, Zhang C, Watkins J, Jin Y, McNutt M, Yin Y.
BMC Bioinformatics. 2016 Apr 5;17(1):153. doi: 10.1186/s12859-016-0998-5.

disCoP – Disorder Consensus-based Predictor

disCoP

:: DESCRIPTION

disCoP method is designed for in-silico prediction of per-residue protein disorder propensities. It combines four rationally selected input predictors: DISOclust, DISOPRED2, MD, and SPINE-D, using custom-designed features that aggregate their predictions and binomial deviance-based regression model.

::DEVELOPER

Kurgan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Biomol Struct Dyn. 2014;32(3):448-64. doi: 10.1080/07391102.2013.775969. Epub 2013 Mar 27.
Accurate prediction of disorder in protein chains with a comprehensive and empirically designed consensus.
Fan X1, Kurgan L.

CSpritz 1.2 – Prediction of Protein Disorder with 3 Separate Predictors

CSpritz 1.2

:: DESCRIPTION

CSpritz is a web server for the prediction of intrinsic protein disorder.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W190-6. doi: 10.1093/nar/gkr411. Epub 2011 Jun 6.
CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs.
Walsh I1, Martin AJ, Di Domenico T, Vullo A, Pollastri G, Tosatto SC.

GlobPlot / GlobPipe 2.3 – Explore Disorder or Globularity in Protein Sequences

GlobPlot / GlobPipe 2.3

:: DESCRIPTION

GlobPlot is a server for exploring disorder or globularity in protein sequences.GlobPlot may be useful in domain hunting efforts. The plots indicate that instances of known domains may often contain additional N- or C-terminal segments that appear ordered.

GlobPipe is a pipeline that can be used for proteome scale analysis.

::DEVELOPER

Gibson Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • Biopython
  • TISEAN

:: DOWNLOAD

 GlobPlot / GlobPipe

:: MORE INFORMATION

Citation

Rune Linding, Robert B. Russell, Victor Neduva and Toby J. Gibson
GlobPlot: exploring protein sequences for globularity and disorder
Nucleic Acid Res 2003 – Vol. 31, No.13

DisEMBL 1.5 – Protein Disorder Prediction

DisEMBL 1.5

:: DESCRIPTION

DisEMBL is a protein disorder prediction software based on neural networks. Predicts propensity for loops (no helix, no strand), hot loops (floppy loops with high temperature factors), and disordered regions (called “Remark465” in DISEMBL).

::DEVELOPER

Rune Linding & Lars Juhl Jensen – EMBL

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DisEMBL

:: MORE INFORMATION

Citation:

R. Linding, L.J. Jensen, F. Diella, P. Bork, T.J. Gibson and R.B. Russell
Protein disorder prediction: implications for structural proteomics
Structure Vol 11, Issue 11, 4 November 2003