- 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.
- 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/
- 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 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 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.
- CABS-NMR toolkit is a package of useful tools for NMR data formats conversion and utilizing sparse NMR data in protein structure modeling. It includes bash scripts for conversion of NMRSTAR format to DipoCoup
formats. An efficient tool called TRANSFORM translates all atom cooridinates of psi and phi dihedral angles into theta and gamma pseudoangles
defined in reduced coordinates of C-alpha backbone trace. Protein structure modeling is performed by CABS-NMR, a modified version of the CABS algorithm, and NMR_FILTER tool which is used to discriminate protein models with respect to such sparse NMR data as: backbone chemical shifts, RDCs, NOEs (including also methyl-methyl NOEs), H/D exchange rates and hydrogen bonds. CONTACT_FILTER is an additional tool which enables to discriminate protein models with respect to predicted contact maps. In case of any questions, please contact: pledor at chem.uw.edu.pl.
D. Latek, D. Ekonomiuk, A. Kolinski, J. Comput. Chem. 28(10) 1668 - 1676, 2007
D. Plewczynska, A. Kolinski, Macromol. Theory Simulations 14(7): 444 - 451, 2005
D. Latek, A. Kolinski, BMC Structural Biology 8:36, 2008
MSITE - written by Dr. Piotr Rotkiewicz in collaboration with Dr. Wanda Sicińska and Mateusz Kurciński, is a program designed to analyse structural data of liganded and unliganded proteins.
MSITE is a simple command-line program for immediate identification of the nearest neighbors of a given amino acids (for example neighbors of residues that contact ligand
or reorient their SC conformation in the presence of agonist/or antagonist) in any number of compared complexes. The arguments of the MSITE program are the names of protein structures
(in PDB format) and a list of residues to be analyzed. The residues are listed individually for every input PDB structure. The program outputs a consensus list of residues being in contact with
the residues specified in the input list. The contact is defined as a distance of 3.5 Angstroms or less between any pair of protons or heavy atoms of the contacting residues. The output list is
divided and sorted according to the order of residues in the input list, thus allowing immediate identification and comparison of subtle structural differences between functionally important
residues within a family of closely related structures.
To extract archive type:
To compile MSITE program, use ANSI C compiler (e.g. GNU C):
cc msite.c -lm -o msite
To run msite, type:
./msite list.txt > output.txt
The program expects the input PDB files to be present in the working directory. Example input files are included in the program archive.URL: http://biocomp.chem.uw.edu.pl/download.php?id=142
- CCOMP is a simple command-line program for comparing ligand/receptor complexes. The program can be used for calculating pairwise all-atom RMSD of slightly different protein structures, taking care of missing atoms, sequence inconsistencies, and other problems often encountered in PDB files. CCOMP can read two files in PDB format, including both a receptor and a ligand, compute a pairwise sequence alignment of the receptor molecules, generate alpha-carbon superposition of the receptor structures according to the generated alignment, and calculate individual deviations per residuum. Additionally, several statistical measures are provided in the input file.URL: http://biocomp.chem.uw.edu.pl/download.php?id=145