1. SURPASS model
  2. BioShell package
  3. BBQ program
  4. Non-redundant PDB subsets

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:

BioShell provides also binding to Python scripting language. The library, precompiled for Python version 2.7, 3.5 and 3.7 may be downloaded from this page

The legacy BioShell 2.0 version may be downloaded from this page. Note, that the single bioshell.bioinformatics-2.2.jar file is a JAVA archive, containing whole BioShell library and all executables. bioshell.bioinformatics-2.2-mono.jar contains definition of macromolecular monomers (amino acids, bases, ligands, etc.). Both files must be added to your CLASSPATH before using BioShell 2.2.


BBQ : backbone building from quadrilaterals

BBQ (Backbone Building from Quadrulaterals) is a program which reads a C-alpha only protein structure and reconstructs protein main chain, i.e. peptide plate atoms. Beta carbon positions are also recovered. At the moment only the BioShell 2.2 version of BBQ is available. To use it, downlad the JAVA archives listed above: bioshell.bioinformatics-2.2.jar and bioshell.bioinformatics-2.2-mono.jar. A working example is also provided on this page.