LR_PPI – large-scale Prediction of Human protein-protein interaction

LR_PPI

:: DESCRIPTION

LR_PPI is a web server for large-scale prediction of human protein-protein interaction from amino acid sequence based on latent topic feature

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

J Proteome Res. 2010 Oct 1;9(10):4992-5001. doi: 10.1021/pr100618t.
Large-scale prediction of human protein-protein interactions from amino acid sequence based on latent topic features.
Pan XY1, Zhang YN, Shen HB.

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.

AutoChrom3D v1 – Modeling and Visualization the 3D Structure of Human or Mouse Chromatin

AutoChrom3D v1

:: DESCRIPTION

AutoChrom3D was built for modeling and visualization the 3D structure of human or mouse chromatin. The 3D structure of chromatin is calculated and generated based on HiC data.

::DEVELOPER

PENG Cheng (email: pengcheng@mail.hzau.edu.cn).

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Perl
:: DOWNLOAD

  AutoChrom3D 

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Oct;41(19):e183. doi: 10.1093/nar/gkt745. Epub 2013 Aug 21.
The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling.
Peng C1, Fu LY, Dong PF, Deng ZL, Li JX, Wang XT, Zhang HY.

NetGene 2.42 – Intron Splice Sites in Human, C. Elegans & A. Thaliana DNA

NetGene 2.42

:: DESCRIPTION

NetGene2 is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

NetGene2 Source Code

:: MORE INFORMATION

Citation

S.M. Hebsgaard, P.G. Korning, N. Tolstrup, J. Engelbrecht, P. Rouze, S. Brunak
Splice site prediction in Arabidopsis thaliana DNA by combining local and global sequence information
Nucleic Acids Research, 1996, Vol. 24, No. 17, 3439-3452.

Brunak, S., Engelbrecht, J., and Knudsen, S.
Prediction of Human mRNA Donor and Acceptor Sites from the DNA Sequence
Journal of Molecular Biology, 1991, 220, 49-65.

LocFuse – Human protein-protein Interaction Prediction

LocFuse

:: DESCRIPTION

LocFuse is a novel ensemble learning method of human protein-protein interaction prediction via classifier fusion using protein localization information.

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • JRE

:: DOWNLOAD

 LocFuse

:: MORE INFORMATION

Citation

LocFuse: human protein-protein interaction prediction via classifier fusion using protein localization information.
Zahiri J, Mohammad-Noori M, Ebrahimpour R, Saadat S, Bozorgmehr JH, Goldberg T, Masoudi-Nejad A.
Genomics. 2014 Dec;104(6 Pt B):496-503. doi: 10.1016/j.ygeno.2014.10.006.

CanProVar 2.0 – Human Cancer Proteome Variation Database

CanProVar 2.0

:: DESCRIPTION

CanProVar is designed to store and display single amino acid alterations including both germline and somatic variations in the human proteome, especially those related to the genesis or development of human cancer based on the published literatures.

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation.
Zhang M, Wang B, Xu J, Wang X, Xie L, Zhang B, Li Y, Li J.
J Proteome Res. 2017 Feb 3;16(2):421-432. doi: 10.1021/acs.jproteome.6b00505.

SPIKE – Database of highly curated human Signaling Pathways

SPIKE

:: DESCRIPTION

SPIKE (Signaling Pathways Integrated Knowledge Engine) is a database of highly curated human signaling pathways with an associated interactive software tool.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

SPIKE: a database of highly curated human signaling pathways.
Paz A, Brownstein Z, Ber Y, Bialik S, David E, Sagir D, Ulitsky I, Elkon R, Kimchi A, Avraham KB, Shiloh Y, Shamir R.
Nucleic Acids Res. 2011 Jan;39(Database issue):D793-9. doi: 10.1093/nar/gkq1167.

GAPI – Explores Hyperbolic Mapping of the human Potein Interaction Network

GAPI

:: DESCRIPTION

GAPI (Geometric Analysis of the Protein Interactome) is a web tool for the geometric analysis of the hPIN.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Aug 15;34(16):2826-2834. doi: 10.1093/bioinformatics/bty206.
The latent geometry of the human protein interaction network.
Alanis-Lobato G, Mier P1,2, Andrade-Navarro M.

HIPPIE 2.2 – study and filter the Network of Human Protein-protein Interaction data

HIPPIE 2.2

:: DESCRIPTION

HIPPIE (Human Integrated Protein-Protein Interaction rEference) is a human PPI dataset with a normalized scoring scheme that integrates multiple experimental PPI datasets.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 HIPPIE

:: MORE INFORMATION

Citation

HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks.
Alanis-Lobato G, Andrade-Navarro MA, Schaefer MH.
Nucleic Acids Res. 2017 Jan 4;45(D1):D408-D414. doi: 10.1093/nar/gkw985

PLoS One. 2012;7(2):e31826. doi: 10.1371/journal.pone.0031826. Epub 2012 Feb 14.
HIPPIE: Integrating protein interaction networks with experiment based quality scores.
Schaefer MH1, Fontaine JF, Vinayagam A, Porras P, Wanker EE, Andrade-Navarro MA.

PIPs 1.1 – Human Protein-Protein Interaction Predictions

PIPs 1.1

:: DESCRIPTION

PIPs is a database of predicted human protein-protein interactions. The predictions have been made using a na?ve Bayesian classifier to calculate a Score of interaction.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

 NO

:: MORE INFORMATION

Citation

PIPs: human protein–protein interaction prediction database
Mark D. McDowall, Michelle S. Scott and Geoffrey J. Barton
Nucl. Acids Res. (2009) 37 (suppl 1): D651-D656. doi: 10.1093/nar/gkn870