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.

BioShell versions. 1.x

The original BioShell package was designed as a suite of programs designed for pre- and post-processing in protein structure modeling protocols. The package has been providing a convenient set of tools for in conversion between various sequence and structure formats. It has been also possible to calculate simple properties of protein conformations. The very first commands (e.g. HCPM for clustering protein structures) were implemented in C, later on the development switched to C++.

BioShell versions 2.x

Around 2006/07 BioShell has been reimplemented in JAVA, designed as a library for scripting languages running on Java Virtual Machine, most notably Python, but also Scala, Ruby, Groovy and many others. Currently the most recent stable release is 2.2. API docs as well as example scripts may be found in documentation. All program from 1.x versions were also ported to JAVA.

BioShell version 3.x


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

Citing BioShell

  • BioShell - the first version:
    D. Gront and A. Kolinski “BioShell - a package of tools for structural biology computations” Bioinformatics 2006 22(5):621-622

  • BioShell - the second version:
    D. Gront and A. Kolinski “Utility library for structural bioinformatics” Bioinformatics 2008 24(4):584-585

  • Program for clustering protein structures (currently named clust):
    D. Gront and A. Kolinski “HCPM - program for hierarchical clustering of protein models” Bioinformatics 2005 21(14):3179-3180

  • BBQ - program for backbone reconstruction:
    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

  • One-dimensional protein threading:
    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

  • Three-dimensional protein threading:
    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