Tag: Structural Bioinformatics

p3d 0.4.3 – Python module for Structural Bioinformatics

p3d 0.4.3

:: DESCRIPTION

p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files).

::DEVELOPER

CELLULAR AND MOLECULAR FUNCTIONS OF REACTIVE OXYGEN SPECIES

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Python

:: DOWNLOAD

  p3d

:: MORE INFORMATION

Citation

Christian Fufezan and Michael Specht
p3d – Python module for structural bioinformatics
BMC Bioinformatics 2009, 10:258 doi:10.1186/1471-2105-10-258

ballaxy – Galaxy-based workflow toolkit for Structural Bioinformatics

ballaxy

:: DESCRIPTION

ballaxy is a workflow framework for structure based computational biology based on the Galaxy workflow engine.

::DEVELOPER

BALL Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Windows
  • Web Server
  • C++ Comipiler

:: DOWNLOAD

 ballaxy

:: MORE INFORMATION

Citation:

ballaxy: web services for structural bioinformatics.
Hildebrandt AK, Stöckel D, Fischer NM, de la Garza L, Krüger J, Nickels S, Röttig M, Schärfe C, Schumann M, Thiel P, Lenhof HP, Kohlbacher O, Hildebrandt A.
Bioinformatics. 2014 Sep 2. pii: btu574.

Biskit 2.4.0 – Python Platform for Structural Bioinformatics

Biskit 2.4.0

:: DESCRIPTION

Biskit is a modular, object-oriented Python library for structural bioinformatics research. It facilitates the manipulation and analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories. For efficient number crunching, Biskit objects tightly integrate with numpy (Numeric Python). Biskit also offers a platform for the rapid integration of external programs and new algorithms into complex workflows. Calculations are thus often delegated to established programs like Xplor, Amber, Hex, Prosa, Fold-X, T-Coffee, Hmmer and Modeller; interfaces to further software can be added easily. Moreover, Biskit simplifies the parallelisation of calculations via PVM (Parallel Virtual Machine).

::DEVELOPER

Biskit Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Python

:: DOWNLOAD

  Biskit

:: MORE INFORMATION

Citation:

Grünberg R, Nilges M and Leckner J. (2007)
“Biskit – A software platform for structural bioinformatics.”
Bioinformatics 23(6), 769-70