In collaboration with the National Institutes of Health, Bethesda, MD, USA we have developed http://charmming.org, a web interface to prepare input files for the CHARMM (Chemistry at HARvard Macromolecular Machaniscs) program. Some of the programs which run the web site were developed at the National Institute of Chemistry.
COBISS.SI-ID: 3983386
A force field of the triclinic framework of AlPO4-34, important in methanol-hydrocarbon conversion reactions, was developed using an empirical potential function. The new force field permits detailed molecular dynamics simulations of flexible, charged aluminophosphate molecular sieves.
COBISS.SI-ID: 3707418
A class of interconnection networks for efficient parallel MD simulations based on Hamiltonian cubic symmetric graphs is presented. Analyzing these communication routines shows that Hamiltonian cubic symmetric graphs of small diameter are good candidates for a topology that gives rise to an interconnection network with excellent properties, allowing faster communication and thus speeding up parallel MD simulation.
COBISS.SI-ID: 3964698
Prediction of protein binding sites is important for the developement of new drugs targeting protein-protein interactions. We show unambiguously for the first time that protein-protein binding sites are structurally conserved. A new algorithm to predict protein-protein binding sites using conservation of both protein surface structure and physical-chemical properties in structurally similar proteins was developed. The predicted binding sites and the actual binding sites are in good agreement. Our algorithm is a useful tool for the prediction of protein binding sites.
COBISS.SI-ID: 4395802
We have also developed a web-tool, available at http://probis.cmm.ki.si for protein binding sites detection, which implements methods described in publication above.
COBISS.SI-ID: 4404506