CABS - CABS is a versatile reduced representation tool for molecular modeling, including: de novo folding of small proteins, comparative modeling (especially in cases of poor templates) and structure prediction based on sparse experimental data. As restraints one may use experimental restraints, restraints from templates, or theoretically predicted restraints (for instance predicted side chain - side chain contacts). Description of the model could be found in recent publications:
the most detailed description in: A. Kolinski, Acta Biochimica Polonica 2004, 51:349-371 available on-line, description of CABS performance during CASP6: A. Kolinski, J.M. Bujnicki, Proteins 2005, 61(S7):84-97 available on-line.
Other publications on CABS applications could be found on our site: list of publications.

Force field parameters can be viewed here: parameters of the CABS model. The full package, including the Linux executable of CABS program, force field data, example input and output files can be downloaded as a tar.gz archive by following the link below.

URL: http://biocomp.chem.uw.edu.pl/download.php?id=100

BioShell - BioShell is a suite of programs performing common tasks accompanying protein structure modeling. BioShell design is based on UNIX shell flexibility and should be used as its extension. Using BioShell various molecular modeling procedures can be integrated in a single pipeline.

URL: http://bioshell.chem.uw.edu.pl/

BBQ - BBQ is a program for protein backbone reconstruction that comprises very high computational efficiency with high accuracy. The details and careful design of the present approach and lead to the algorithm that outperforms all commonly used earlier applications. BBQ program has been extensively tested both on native structures as well as on near-native decoy models and compared with the different available existing methods: Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates.

URL: http://www.biocomp.chem.uw.edu.pl/services/BBQ/

biodesigner - Biodesigner is a free, open source, general purpose molecular visualization and modeling program. The application is particularly useful for design and analysis of 3D protein models and simulation trajectories. The program is coupled with sequence alignment editor and molecular mechanics engine.

URL: http://www.pirx.com/biodesigner/

iMol - iMol is a lighweight molecule viewer for Apple Mac OS X operating system. The program is well integrated with Aqua user interface and it offers basic visualization and structure analysis capabilities.

URL: http://www.pirx.com/iMol/

HCPM - HCPM is a program which finds groups of similar structures in a large set of protein models. Similarity between structures could be measured by crmsd (coordinate root-mean-square deviation) or by drmsd (distance root-mean-square deviation). Clustering needs to be performed only once. During the clustering a hierarchy describing similarity of the structures is stored in an external file. Using this file it is possible to recalculate clusters for different input settings without any noticeable additional computational cost.

URL: http://www.biocomp.chem.uw.edu.pl/HCPM