Computational software has been a cornerstone of many biological sciences such as biophysics, bioinformatics or biomolecular modelling in general. The last few decades witnessed numerous software packages that implemented newly emerging methods and algorithms. In parallel with the development of methods to solve particular scientific problems, the general picture how a suite of computational software should be constructed also evolved.Here we present the design, implementation and functionality of BioShell[1,2] software - a versatile package for biomolecular modelling. Its functionality ranges from processing structural and sequence databases to sampling conformations both in Cartesian and alignment space. Highly modular structure facilitates easy extension of the package. Its modules may be conveniently bound by a high-level Python script into a single pipeline.One of the newest BioShell applications is three-dimensional threading. A Monte Carlo search scheme samples the conformational space of alignments between a query sequence and a template structure. In another example, BioShell modules were used to build a simple computational model of RNA molecules.1. D. Gront, and A. Kolinski, Bioinformatics, 2005, 22, 621-622.2. D. Gront, and A. Kolinski, Bioinformatics, 2008, 24, 584-585.