PredAlgo 1.0 – Protein Subcellular Localization Prediction in Green Algae

PredAlgo 1.0

:: DESCRIPTION

PredAlgo is a new sequence analysis tool, dedicated to the prediction of protein subcellular localization in green algae. It uses a neural network trained with carefuly curated sets of Chlamydomonas reinhardtii proteins. PredAlgo predicts the localization to one of three compartments: the mitochondrion, the chloroplast, the secretory pathway within the cell.

::DEVELOPER

Nicolas J. Tourasse or Olivier Vallon

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Mol Biol Evol. 2012 Dec;29(12):3625-39. doi: 10.1093/molbev/mss178.
PredAlgo: a new subcellular localization prediction tool dedicated to green algae.
Tardif M, Atteia A, Specht M, Cogne G, Rolland N, Brugière S, Hippler M, Ferro M, Bruley C, Peltier G, Vallon O, Cournac L.

COMSPA – Predicting Protein Structural Classes from Primary Sequence

COMSPA

:: DESCRIPTION

COMSPA is a web server for predicting protein structural classes from primary sequence by learning multi-view features in complex space

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Amino Acids. 2013 May;44(5):1365-79. doi: 10.1007/s00726-013-1472-6. Epub 2013 Feb 28.
Learning protein multi-view features in complex space.
Yu DJ1, Hu J, Wu XW, Shen HB, Chen J, Tang ZM, Yang J, Yang JY.

LnSignal – Predicting Protein N-terminal Signal Peptides

LnSignal

:: DESCRIPTION

The web server LnSignal (Labelling N-terminal Signal petide cleavage site) was developed by integrating position-specific amino acid propensities based on the highest average positions and conditional random fields.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Yong-Xian Fan, Jiangning Song, Chen Xu and Hong-Bin Shen,
Predicting protein N-terminal signal peptides using position-specific amino acid propensities and conditional random fields ,
Current Bioinformatics, 2013, 8: 183-192.

Nuc-PLoc – Predicting Protein Subnuclear Localization

Nuc-PLoc

:: DESCRIPTION

Nuc-PLoc is a new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nuc-PLoc: a new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM.
Shen HB, Chou KC.
Protein Eng Des Sel. 2007 Nov;20(11):561-7. Epub 2007 Nov 10.

PFP-FunDSeqE – Predicting Protein Fold Pattern

PFP-FunDSeqE

:: DESCRIPTION

PFP-FunDSeqE is a web server of predicting protein fold pattern with functional domain and sequential evolution information

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

J Theor Biol. 2009 Feb 7;256(3):441-6. doi: 10.1016/j.jtbi.2008.10.007. Epub 2008 Oct 19.
Predicting protein fold pattern with functional domain and sequential evolution information.
Shen HB1, Chou KC.

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.

PFP-Pred 2.0 – Protein Fold Prediction

PFP-Pred 2.0

:: DESCRIPTION

PFP-Pred is an ensemble classifier for protein fold pattern recognition

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Hong-Bin Shen and Kuo-Chen Chou,
Ensemble classifier for protein folding pattern recognition“.
Bioinformatics, 2006, 22: 1717-22.

ConSurf 2016 – Identification of Functional Regions in Proteins

ConSurf 2016

:: DESCRIPTION

The ConSurf server is a bioinformatics tool for estimating the evolutionary conservation of amino/nucleic acid positions in a protein/DNA/RNA molecule based on the phylogenetic relations between homologous sequences.

::DEVELOPER

Mayrose Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Ashkenazy H., Abadi S., Martz E., Chay O., Mayrose I., Pupko T., and Ben-Tal N. 2016
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules
Nucl. Acids Res. 2016; DOI: 10.1093/nar/gkw408; PMID: 27166375

Ashkenazy H., Erez E., Martz E., Pupko T. and Ben-Tal N. 2010
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids.
Nucl. Acids Res. 2010; DOI: 10.1093/nar/gkq399; PMID: 20478830

SOLart 1.0 – Protein Solubility Prediction

SOLart 1.0

:: DESCRIPTION

SOLart is a fast and accurate method for predicting the protein solubility of a target protein whose experimental or modeled structure is available. It yields a scaled solubility score with values close to zero indicating aggregate-prone proteins, while values close to 130 designate soluble proteins.

::DEVELOPER

Service de Biomodélisation, Bioinformatique et Bioprocédés (3BIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics, 36 (5), 1445-1452 2020 Mar 1
SOLart: A Structure-Based Method to Predict Protein Solubility and Aggregation
Qingzhen Hou , Jean Marc Kwasigroch, Marianne Rooman, Fabrizio Pucci

SCooP 1.0 – Prediction of the Stability Curve of Proteins

SCooP 1.0

:: DESCRIPTION

SCooP is a fast and accurate method for predicting the Gibbs-Helmholtz equation associated to the folding transition of a target protein of known (or modeled) structure. In addition, SCooP yields an estimation of the thermodynamic quantities that characterize the folding process, in particular the change in enthalpy and in heat capacity upon folding, the melting temperature and the folding free energy at room temperature.

::DEVELOPER

Service de Biomodélisation, Bioinformatique et Bioprocédés (3BIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

F. Pucci, J.M. Kwasigroch, M. Rooman (2017),
SCooP : an accurate and fast predictor of protein stability curves as a function of the temperature,
Bioinformatics 33, 3415-3422.