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Welcome to Biskit!

A Python platform for structural bioinformatics

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, DSSP, Fold-X, T-Coffee, TMAlign and Modeller; interfaces to further software can be added easily. Biskit also simplifies the parallelisation of calculations via PVM (Parallel Virtual Machine).


What can Biskit do for you?

Here is an overview over some typical workflows that are realised in Biskit (PDBModel, PDBDope, Trajectory, and ComplexList are prominent classes of the package, the whole library is fully object-oriented):

Biskit workflow

A few examples of what you can do with Biskit:

  • analyze molecular structures, complexes and molecular dynamics trajectories
  • automated conformal sampling
  • automated homology modeling
  • multi-model protein-protein (cross-)docking
  • quasiharmonic entropy calculations
  • parallelise and automate your own structural bioinformatics workflows

But remember the famous words - Ask not what Biskit can do for you, ask ...
How to contribute



If something doesn't work according to plan or promise, browse this web site (the search button in the top right corner is very useful) but feel also free to directly contact us!

FAQ      Search & report bugs       Mailing list      Contact us



Biskit has been jointly developed by Raik Grünberg and Johan Leckner (then at the Pasteur Institute in Paris) with important contributions from Michael Habeck (now Max-Planck-Institut für Entwicklungsbiologie, Tuebingen, Germany), Michael Nilges (Institut Pasteur), Wolfgang Rieping (Institut Pasteur) and others.

Detailed contributions     How to contribute


License and availability

Biskit is freely available under the terms of the GNU General Public License (v. 3). The latest official Biskit release is available from our github project site.  It can be installed with:

pip install biskit

A more current (and usually better) snapshot can be fetched from github as described here. There are also Debian and RPM packages available with most releases. See Short Installation Instructions.