iLocator – An Image-based Multi-label Human Protein Subcellular Localization Predictor

iLocator

:: DESCRIPTION

iLocator is an image-based multi-label subcellular location predictor, which covers 7 cellular localizations, i.e. cytoplasm, endoplasmic reticulum, Golgi apparatus, lysosome, mitochondria, nucleus, and vesicles. The iLocator incorporates both global and local image descriptors, and uses an ensemble multi-label classifier to generate accurate predictions.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

iLocator

:: REQUIREMENTS

  • Windows
  • Matlab

:: DOWNLOAD

 iLocator

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Aug 15;29(16):2032-40. doi: 10.1093/bioinformatics/btt320. Epub 2013 Jun 4.
An image-based multi-label human protein subcellular localization predictor (iLocator) reveals protein mislocalizations in cancer tissues.
Xu YY1, Yang F, Zhang Y, Shen HB.

TargetSOS – Supervised Over-sampling Predictor for Targeting Protein-nucleotide Binding Residues

TargetSOS

:: DESCRIPTION

TargetSOS is a predictor based on the proposed over-sampling algorithm which implemented for protein-nucleotide binding residue prediction.

::DEVELOPER

Pattern Recognition and Bioinformatics Group (Shen Group)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

A new supervised over-sampling algorithm with application to protein-nucleotide binding residue prediction.
Hu J, He X, Yu DJ, Yang XB, Yang JY, Shen HB.
PLoS One. 2014 Sep 17;9(9):e107676. doi: 10.1371/journal.pone.0107676.

SOMRuler – A Novel Interpretable Transmembrane Helices Predictor

SOMRuler

:: DESCRIPTION

SOMRuler is a novel TMH predictor with excellent interpretability while possessing high prediction accuracy.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 SOMRuler

:: MORE INFORMATION

Citation:

IEEE Trans Nanobioscience. 2011 Jun;10(2):121-9. doi: 10.1109/TNB.2011.2160730. Epub 2011 Jul 7.
SOMRuler: a novel interpretable transmembrane helices predictor.
Yu D, Shen H, Yang J.

GraPPLE – Graph Property based Predictor and Likelihood Estimator

GraPPLE

:: DESCRIPTION

GraPPLE are abstract representations of relationships between entities. Through a set of instructions, they are able to convert relationships into nodes and edges. GraPPLE (originally: The RNA sorting hat) leverages the information available from graph properties and the predictive power of support vector machines (SVMs) to classify potential RNA sequences as functional/non-functional and into 1 of 46 Rfam families. In short, GraPPLE predicts the potential function of an ncRNA sequence.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 May;37(9):e66. Epub 2009 Apr 1.
Identification and classification of ncRNA molecules using graph properties.
Childs L, Nikoloski Z, May P, Walther D.

PCTpred – PTM Cross-Talk predictor

PCTpred

:: DESCRIPTION

PCTpred is a computational method that can accurately identify PTM cross-talk pairs in a given protein sequence or structure.

::DEVELOPER

Rong Liu’s Lab of Protein Bioinformatics at Huazhong Agriculture University!

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Perl
:: DOWNLOAD

PCTpred

:: MORE INFORMATION

Citation:

Brief Bioinform 2019 Jan 11
Structure-based Prediction of Post-Translational Modification Cross-Talk Within Proteins Using Complementary Residue- And Residue Pair-Based Features
Hui-Fang Liu 1, Rong Liu 1

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

GOMEP – Gene Ontology-based Missing Enzyme Predictor

GOMEP

:: DESCRIPTION

GOMEP Predicts Missing Enzymes using functional coherence scores of Gene Ontology (GO) terms

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

GOMEP

:: MORE INFORMATION

Citation

Sci Rep. 2016 Aug 24;6:31725. doi: 10.1038/srep31725.
Missing gene identification using functional coherence scores.
Chitale M, Khan IK, Kihara D

Phobius /PolyPhobius 1.05 – Combined Transmembrane Topology & Signal Peptide Predictor

Phobius /PolyPhobius 1.05

:: DESCRIPTION

Phobius /PolyPhobius is for prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein.

::DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Phobius

:: MORE INFORMATION

Citation:

Phobius is described in:

  • Lukas Käll, Anders Krogh and Erik L. L. Sonnhammer.
    A Combined Transmembrane Topology and Signal Peptide Prediction Method.
    Journal of Molecular Biology, 338(5):1027-1036, May 2004.
    (doi) (PubMed)

PolyPhobius is described in:

  • Lukas Käll, Anders Krogh and Erik Sonnhammer.
    An HMM posterior decoder for sequence feature prediction that includes homology information
    Bioinformatics, 21 (Suppl 1):i251-i257, June 2005.
    (doi) (PubMed)

 

ZincExplorer – Predictor of Protein Zinc-binding Sites

ZincExplorer

:: DESCRIPTION

ZincExplorer is a web server that could predict Zinc-binding sites from protein sequence.

::DEVELOPER

Ziding Zhang’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Mol Biosyst. 2013 Sep;9(9):2213-22. doi: 10.1039/c3mb70100j.
ZincExplorer: an accurate hybrid method to improve the prediction of zinc-binding sites from protein sequences.
Chen Z, Wang Y, Zhai YF, Song J, Zhang Z.

SPAR v1.0 – Predictor for self-interacting protein from Sequence Information

SPAR v1.0

:: DESCRIPTION

SPAR (Self-interacting Protein AnalyzeR) was a predictor for self-interacting protein from sequence information. Based on comprehensive analysis of a variety of physiochemical properties on self-interacting proteins, a new encoding scheme named RSI has been designed.

::DEVELOPER

Ziding Zhang’s Lab, China Agricultural University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SPAR

:: MORE INFORMATION

Citation

Amino Acids. 2016 Jul;48(7):1655-65. doi: 10.1007/s00726-016-2226-z.
SPAR: a random forest-based predictor for self-interacting proteins with fine-grained domain information.
Liu X, Yang S, Li C, Zhang Z, Song J.