MPRAP – Membrane Protein Residue Accessibility Predictor

MPRAP

:: DESCRIPTION

MPRAP is a novel Membrane Protein Residue Accessibility Predictor, based on sequence derived information. In contrast to previous membrane predictors, MPRAP, performs well both within and outside the membrane regions and outperforms earlier methods in the membrane regions.

::DEVELOPER

Elofsson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Jun 18;11:333. doi: 10.1186/1471-2105-11-333.
MPRAP: an accessibility predictor for a-helical transmembrane proteins that performs well inside and outside the membrane.
Illergård K1, Callegari S, Elofsson A.

CELLO v.2.5 / CELLO2GO – subCELlular LOcalization predictor

CELLO v.2.5 / CELLO2GO

:: DESCRIPTION

CELLO is a multi-class SVM classification system. CELLO uses 4 types of sequence coding schemes: the amino acid composition, the di-peptide composition, the partitioned amino acid composition and the sequence composition based on the physico-chemical properties of amino acids. We combine votes from these classifiers and use the jury votes to determine the final assignment.

CELLO2GO is a publicly available, web-based system for screening various properties of a targeted protein and its subcellular localization.

::DEVELOPER

CELLO team,  National Chiao Tung University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CELLO2GO: a web server for protein subCELlular LOcalization prediction with functional gene ontology annotation.
Yu CS, Cheng CW, Su WC, Chang KC, Huang SW, Hwang JK, Lu CH.
PLoS One. 2014 Jun 9;9(6):e99368. doi: 10.1371/journal.pone.0099368.

Protein Sci. 2004 May;13(5):1402-6.
Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions.
Yu CS, Lin CJ, Hwang JK.

ILbind – Consensus-based Inverse Ligand Binding Predictor

ILbind

:: DESCRIPTION

ILbind is a consensus predictor that combines the two complementary inverse ligand binding predictors implemented using FINDSITE and SMAP and Support Vector Machines.

::DEVELOPER

Kurgan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ILbind

:: MORE INFORMATION

Citation

Hu G, Gao J, Wang K, Mizianty MJ, Ruan J, Kurgan L.
Finding protein targets for small biologically relevant ligands across fold space using inverse ligand binding predictions.
Bioinformatics. 2014 Aug 28. pii: btu581. [Epub ahead of print]

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

:: 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