PROTEIN MODELING & STRUCTURAL GENOMICS

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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 goal of the protein modeling project of the MMTSB resource aims at developing a multi-scale modeling approach to protein structure prediction, fragment and loop modeling, as well as structure refinement of approximate structures derived by other methods. For lattice-based low-resolution modeling the MONSSTER program by Kolinski and Skolnick is used and distributed as part of the MMTSB Tool Set. In this model proteins are represented with a single particle for each residue located at the side chain center and are simulated with a Monte Carlo scheme on a cubic lattice. More recently, the project has been extended to include the newest generation structure prediction tools PROSPECTOR3/TASSER/SPICKER from the Skolnick lab. All-atom modeling is performed using CHARMM with an implicit solvent model based on a Generalized Born approximation. This allows rapid energy evaluations for all-atom structures and offers the possibility of fast all-atom simulations for further structure refinement.