Tag: Plug-In

Cytoprophet 1.0 – A Cytoscape plug-in for Protein and Domain Interaction Networks Inference

Cytoprophet 1.0

:: DESCRIPTION

Cytoprophet is a project developed by the Laboratory for Computational Life Sciences at the Computer Science Department of the University of Notre Dame. It is a tool to help researchers to infer new potential protein (PPI) and domain (DDI) interactions. It is implemented as a Cytoscape plugin, where users input a set of proteins and retrieve a network of plausible protein and domain interactions with a score. Three algorithms are used for the estimation of PPI/DDI: Maximum Specificity Set Cover (MSSC) Approach, Maximum Likelihood Estimation (MLE) and the Sum-Product Algorithm (SPA) for protein networks.

::DEVELOPER

Cytoprophet team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Cytoprophet

:: MORE INFORMATION

Citation

Chengbang Huang , Faruck Morcos, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, and Jesús A. Izaguirre
Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol 4 pp. 78-87. Jan-March 2007

AxPyMOL 2.5 – PowerPoint Plug-In for Embedding 3D Molecular Images & Animations

AxPyMOL 2.5

:: DESCRIPTION

AxPyMOL, a plugin for Windows PowerPoint that enables presentation of 3-D molecular data without having to “tab out” of PowerPoint slides.

AxPyMOL allows users to easily embed PyMOL shows saved from actual PyMOL sessions directly into PowerPoint slides. During presentation, the PyMOL shows can be manipulated within PowerPoint to display structures using multiple vantage points and rendering schemes set up in advance. Users can simply advance through the saved scenes of a PyMOL show without ever exiting PowerPoint.

::DEVELOPER

Schrödinger, LLC

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Office

:: DOWNLOAD

AxPyMOL

:: MORE INFORMATION

PyDeT – PyMOL Plug-in for Visualizing Geometric Concepts around Proteins

PyDeT

:: DESCRIPTION

PyDeT is a plug-in for PyMOL capable of visualizing Delaunay tessalations of atom sets.

::DEVELOPER

PIT Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Python
  • PyMol

:: DOWNLOAD

 PyDeT

:: MORE INFORMATION

Citation

Bioinformation. 2008 May 27;2(8):346-7.
PyDeT, a PyMOL plug-in for visualizing geometric concepts around proteins.
Ordog R

BiNoM 2.5 – Cytoscape plug-in for Manipulating and Analysing biological networks

BiNoM 2.5

:: DESCRIPTION

BiNoM (Biological Network Manager )is a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats (SBML, SBGN, BioPAX) and to carry out studies on the network structure. BiNoM provides the user with a complete interface for the analysis of biological networks in Cytoscape environment.

::DEVELOPER

Computational Systems Biology of Cancer group in Bioinformatics Laboratory of Institut Curie (Paris).

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 BiNoM

:: MORE INFORMATION

Citation:

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats.
Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A.
BMC Syst Biol. 2013 Mar 1;7:18. doi: 10.1186/1752-0509-7-18.

Zinovyev A., Viara E., Calzone L., Barillot E.
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. 2008.
Bioinformatics 24(6):876-877

Pathicular 1.55 – Cytoscape plug-in of Identifies Path Motifs

Pathicular 1.55

:: DESCRIPTION

Pathicularis the Cytoscape plug-in which identifies path motifs in integrated networks and arranges them in a modular structure. After the integrated network and the source network (deletion or overexpression in this case) are loaded into Cytoscape, Pathicular can be used to find all the paths of a given type in the source network using the integrated network. A p-value is provided to check the overrepresentation of the path of interest.

::DEVELOPER

Bioinformatics & Systems Biology

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 Pathicular

:: MORE INFORMATION

Citation:

Genome Biol. 2010;11(3):R32. Epub 2010 Mar 11.
Characterizing regulatory path motifs in integrated networks using perturbational data.
Joshi A, Van Parys T, Peer YV, Michoel T.