Table of Services

Molecular Modeling Facility


The Molecular Modeling Facility provides state-of-the-art services in protein sequence analysis and structure prediction to FCCC investigators. These services include database search, multiple sequence alignment, phylogenetic trees, secondary structure prediction, transmembrane, coiled-coil and disordered region prediction, homology modeling of single proteins and oligomeric complexes, protein-protein and protein-ligand docking, and ligand design.


Currently, more than one half of sequenced proteins are homologous at least in part to a protein of known structure. Homology modeling methods use known structures to build three-dimensional models of target proteins of unknown structure. These models can be used to predict functional interactions with other molecules, to explain existing experimental data, to generate testable hypotheses, and in some cases to become the basis for design of specific inhibitors for translational research. In many cases, it is possible to model homo- and heterooligomers of protein complexes.

The Facility was created in April 2003, and since that time has performed services for over 60 Principal Investigators in all programs at FCCC. The Facility has developed software for automating the modeling process to allow Facility staff more time to concentrate on the biological problem under study in collaboration with the principal investigator. This software is unique in the molecular modeling field in its ability to model oligomeric protein structures from homologous templates.