CellNetAnalyzer 2021.1 – Structural & Functional Analysis of Cellular Networks

CellNetAnalyzer 2021.1

:: DESCRIPTION

CellNetAnalyzer is a package for MATLAB and provides a comprehensive and user-friendly environment for structural and functional analysis of biochemical networks. CNA facilitates the analysis of metabolic (stoichiometric) as well as signaling and regulatory networks solely on their network topology, i.e. independent of kinetic mechanisms and parameters. CNA provides a powerful collection of tools and algorithms for structural network analysis which can be started in a menu-controlled manner within interactive network maps. Recently, API functionalities have been added to enable interested users to call algorithms of CNA from external programs. Applications of CNA can be found in systems biology, biotechnology, metabolic engineering, pharmacology, microbiology, chemical engineering.

::DEVELOPER

Steffen Klamt and Axel von Kamp at theMax Planck Institute for Dynamics of Complex Technical Systems in Magdeburg

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • MATLAB

:: DOWNLOAD

CellNetAnalyzer ; plugins

:: MORE INFORMATION

Citation

Klamt S, Saez-Rodriguez J and Gilles ED (2007)
Structural and functional analysis of cellular networks with CellNetAnalyzer.
BMC Systems Biology 1: 2.

Klamt S and von Kamp A (2011)
An application programming interface for CellNetAnalyzer.
BioSystems 105: 162-168.

VESTA 3.5.7 – 3D Visualization System for Electronic & Structural Analysis

VESTA 3.5.7

:: DESCRIPTION

VESTA (Visualization System for Electronic & Structural Analysis) is a 3D visualization program for structural models and 3D grid data such as electron/nuclear densities. Some of the novel features of VESTA are listed below.

::DEVELOPER

Koichi Momma

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 VESTA

:: MORE INFORMATION

Citation

K. Momma and F. Izumi,
VESTA: a three-dimensional visualization system for electronic and structural analysis,”
J. Appl. Crystallogr., 41:653-658, 2008.

MONGOOSE 1.1 – Structural Analysis and Refinement of Constraint-based Metabolic Networks

MONGOOSE 1.1

:: DESCRIPTION

MONGOOSE (MetabOlic Network GrOwth Optimization Solved Exactly) is a package for structural analysis and refinement of constraint-based metabolic networks. Unlike other existing software, MONGOOSE uses exact rational arithmetic, which makes its results certifiably accurate.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 MONGOOSE

:: MORE INFORMATION

Citation:

Genome Biol. 2012 Jan 31;13(1):r6. doi: 10.1186/gb-2012-13-1-r6.
MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis.
Chindelevitch L, Stanley S, Hung D, Regev A, Berger B.

SAPIN – Structural Analysis of Protein Interaction Networks

SAPIN

:: DESCRIPTION

SAPIN is a framework dedicated to the Structural Analysis of Protein Interaction Networks.SAPIN first identifies the protein parts that could be involved in the interaction and provides template structures. Next, SAPIN performs structural superimpositions to identify compatible and mutually exclusive interactions. Finally, the results are displayed using Cytoscape Web.

::DEVELOPER

Design of Biological Systems Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2998-9. doi: 10.1093/bioinformatics/bts539. Epub 2012 Sep 6.
SAPIN: a framework for the structural analysis of protein interaction networks.
Yang JS1, Campagna A, Delgado J, Vanhee P, Serrano L, Kiel C.

VADAR 1.8 – Structural Analysis of Protein Coordinates

VADAR 1.8

:: DESCRIPTION

VADAR (Volume Area Dihedral Angle Reporter) performs structural analysis of protein coordinate data . It provides the user with objective information on secondary structure, residue volume, accessible surface area as well as phi and psi angles, and hbonds. This data is further collated to provide a summary information and a quality index.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 VADAR

:: MORE INFORMATION

Citation

Leigh Willard, Anuj Ranjan,Haiyan Zhang,Hassan Monzavi, Robert F. Boyko, Brian D. Sykes, and David S. Wishart
VADAR: a web server for quantitative evaluation of protein structure quality
Nucleic Acids Res. 2003 July 1; 31 (13): 3316.3319