Laboratory for Molecular Modeling
We develop and employ innovative molecular modeling approaches to study the structure, dynamics, and function of complex molecular systems.
STOCK
STOCK is a web-based toolkit for setting up coarse-grained molecular simulations. One can define molecular mapping from high to low resolution with the aid of a molecular visualizer. Additionally, one may generate effective potentials for coarse-grained simulations preserving structural properties of the underlying higher resolution model.
The tool is available at http://stock.cmm.ki.si
ENZO
ENZO is a web tool for rapid evaluation of kinetic models of enzyme catalyzed reactions, available at enzo.cmm.ki.si. It automatically generates corresponding differential equations from a stipulated enzyme reaction scheme and fits their coefficients to experimentally observed time course curves.
The ENZO article was published in PLoS ONE.
ProBiS
The ProBiS server for protein binding sites prediction is available at probis.cmm.ki.si and is featured on the RCSB PDB and the Computational Chemistry List websites.
Read the ProBiS articles published in Bioinformatics and Nucleic Acids Research.
CROW
CROW – Columns and Rows Of Workstations
Our lab develops and maintains a computer cluster CROW and workstations with software for computer simulations and modeling.