What is BioShell?

A set of command-line programs for easy data manipulation from a terminal or a shell script. The programs can read and write standard file formats and handle protein sequences and structures. The tools helps also in simple calculations, like sequence alignment, Phi/Psi angles, crmsd and many more. See Programs page for details.

A versatile library for python scripting. BioShell modules can be loaded into any jython implementation written in Java, e.g. Jython. The modules can also be used to develope Java application. See Library modules page for overview of the libary. Example scripts may be found on Scripts library page. At some point one should read BioShell API.
Download all jars (256MB)

History of the BioShell package

BioShell has been designed as a suite of programs designed for pre- and post-processing in protein structure modeling protocols. The package provides a convenient set of tools for in conversion between various sequence and structure formats. It is also possible to calculate simple properties of protein conformations.

The idea, the BioShell is based on, is to enhance Unix shell (e.g. bash) with additional commands, which can be easily combined not only with shell scripts, but also with other scripting languages, as Python or Perl.

Recently the BioShell package has been rewritten in Java language. Now it is much more convenient to keep BioShell platform-independent. Moreover, the development process is faster and more reliable. From the user point of view, the only change concern the names of the BioShell components and the way how they are invoked.

In the newest edition, BioShell has been refactored into a library of modules for biomolecular modeling. The modules can be combined with powerful Python scripting language into a very flexible modeling platform


BioShell is a closed-source package that publicly available for academic non-profit institutions.

Please, cite BioShell as:

D. Gront and A. Kolinski "Utility library for structural bioinformatics" Bioinformatics 2008 24(4):584-585
D. Gront and A. Kolinski "BioShell - a package of tools for structural biology computations" Bioinformatics 2006 22(5):621-622

Using HCPM please cite also:

D. Gront and A. Kolinski "HCPM - program for hierarchical clustering of protein models" Bioinformatics 2005 21(14):3179-3180

Using BBQ please cite also:

D. Gront, S. Kmiecik, A. Kolinski "Backbone Building from Quadrilaterals. A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates." J. Comput. Chemistry 2007 28(9):1593-1597

If you find BioShell-Threader useful in your research please cite two papers:

P. Gniewek, A. Kolinski, D. Gront "Optimization of profile-to-profile alignment parameters for one-dimensional threading." J. Computational Biology 2012 Jul;19(7):879-86

D. Gront, M. Blaszczyk, P. Wojciechowski, A. Kolinski "Bioshell Threader: protein homology detection based on sequence profiles and secondary structure profiles." Nucleic Acids Research 2012 doi:10.1093/nar/gks555