1. BioShell package
  2. SURPASS model

SURPASS model

Single United Residue per Pre-Averaged Secondary Structure fragment is a novel coarse-grained low resolution model for protein simulations. The positions of pseudo residues are defined by averaging the coordinates of short secondary structure fragments, hence the name of the model.
The two relevant articles are listed below:

Dawid A.E., Gront D., Kolinski A.
,,SURPASS Low-Resolution Coarse-Grained Protein Modeling.''
J Chem Theory Comput. 2017 Nov 14;13(11):5766-5779.
Dawid A.E., Gront D., Kolinski A.
,,Coarse-Grained Modeling of the Interplay between Secondary Structure Propensities and Protein Fold Assembly.''
J Chem Theory Comput. 2018 Apr 10;14(4):2277-2287.

The first paper describes the model definition and force field. In the second it has been shown that small inaccuracies in secondary structure definition, which is the only input to the calculations, do not affects quality of predictions. Technical details and up-to-date documentation is now hosted at Read The Docs website.


BioShell package

BioShell is set of command-line programs for easy data manipulation from a terminal or a shell script. BioShell is also a C++ library of bioinformatics and biosimulations classes. Last but not least, BioShell provides also binding to Python scripting language. For practical reasons, documentation of the package has also been moved to Read The Docs. In particular, you can read there: