NaviCell – Web Tool for Exploring large maps of Molecular Interactions

NaviCell

:: DESCRIPTION

NaviCell is a web tool for exploring large maps of molecular interactions created in CellDesigner. The tool is characterized by a unique combination of three essential features: efficient map navigation based on Google maps engine, semantic zooming for viewing different levels of details on the map and an integrated blog for collecting the community curation feedbacks.

::DEVELOPER

NaviCell Team

:: SCREENSHOTS

:: REQUIREMENTS

any web browser

:: DOWNLOAD

no (only web service)

:: MORE INFORMATION

Citation

BMC Syst Biol. 2013 Oct 7;7:100. doi: 10.1186/1752-0509-7-100.
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.
Kuperstein I1, Cohen DP, Pook S, Viara E, Calzone L, Barillot E, Zinovyev A.

Cerebral 2.8.2 / CerebralWeb 1.0 – Cytoscape Molecular Interaction Viewer

Cerebral 2.8.2 / CerebralWeb 1.0

:: DESCRIPTION

Cerebral (Cell Region-Based Rendering And Layout) is a Java plugin for the widely used open-source Cytoscape molecular interaction viewer.

CerebralWeb is a light-weight JavaScript plug-in that extends Cytoscape.js to enable fast and interactive visualisation of molecular interaction networks stratified based on subcellular localisation or other custom annotation.

::DEVELOPER

Cerebral team

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/ MacOsX
Java
Cytoscape

:: DOWNLOAD

Cerebral

:: MORE INFORMATION

Citation

Barsky A, Gardy JL, Hancock REW, and Munzner T. (2007)
Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation.
Bioinformatics 23(8):1040-2.

Database (Oxford). 2015 May 7;2015. pii: bav041. doi: 10.1093/database/bav041. Print 2015.
CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization.
Frias S1, Bryan K1, Brinkman FS1, Lynn DJ

MIEC-SVM 1.1 – Molecular Interaction Energy Component & Support Vector Machine

MIEC-SVM 1.1

:: DESCRIPTION

MIEC-SVM method aims to characterize the energetic patterns of proteins binding to their partners.

::DEVELOPER

Wei Wang’s group

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux
Perl

:: DOWNLOAD

MIEC-SVM

:: MORE INFORMATION

Citation

MIEC-SVM: Automated Pipeline for Protein Peptide/ligand Interaction Prediction.
Li N, Ainsworth RI, Wu M, Ding B, Ainsworth RI, Wang W.
Bioinformatics. 2015 Nov 14. pii: btv666.

GIANT – Pattern analysis of Molecular Interactions in 3D Structures of Protein–small Ligand Complexes

GIANT

:: DESCRIPTION

GIANT (Gaussian mixture model-based Interaction ANalyzer focusing on Three-atom fragments)is a web server for pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes.

::DEVELOPER

GIANT team

:: SCREENSHOTS

N/A

::REQUIREMENTS

Web server

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jan 14;15:12. doi: 10.1186/1471-2105-15-12.
GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes.
Kasahara K, Kinoshita K

InteroPorc 2.0.2 – Automatic Molecular Interaction Predictions

InteroPorc 2.0.2

:: DESCRIPTION

InteroPorc is an automatic prediction tool to infer protein-protein interaction networks. It is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8.

::DEVELOPER

Magali Michaut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / Mac OsX
Java

:: DOWNLOAD

InteroPorc , Source Code

:: MORE INFORMATION

Citation

Magali Michaut, Samuel Kerrien, Luisa Montecchi-Palazzi, Franck Chauvat, Corinne Cassier-Chauvat, Jean-Christophe Aude, Pierre Legrain and Henning Hermjakob,
InteroPORC: Automated Inference of Highly Conserved Protein Interaction Networks
Bioinformatics, 24(14): 1625-1631