This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The Structural Bioinformatics Facility, as part of the Nebraska Informatics Center for the Life Sciences, at the Department of Biomedical Sciences continued to serve faculties and students. The computer clusters, with exceptions for short downtimes for maintenances, are up and running and the Facility is intensively used for structural characterization of peptides using quantum chemical calculations and molecular dynamics simulations. During the year additional Jaguar 5.5 licenses were purchased (we now have a total of 58 licenses) and the package was extensively used by the BRIN student Nicholas Palermo. During his research, he showed for the first time, interactions between aromatic side chains and the peptide backbone by quantum chemical calculations. His results help to understand how proteins function and these results were presented at the 7th Congress of World Association of Theoretically Oriented Chemists. A small cluster, with 6 dual 2.2 GHz AMD Opteron computers connected through a Myrinet and gigabit switch boxes, was setup and Gaussian03, NWChem 4.5, Gromacs 3.2 packages were installed to widen computational capabilities in the facility. In January 2005, Jozsef Csontos, Ph.D. was hired. His major duties are to maintain the clusters, support researchers and participate in research activities.
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