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Structural and Chemical Biology @ Vanderbilt University |
Development of energy-/scoring-functions determining native-like modeled protein structures
Members: Nils Woetzel, Elizabeth Durham
all research projects
Ab initio modeling of protein structures using a monte carlo algorithm searching for a global minimum in the energy landscape of the possible foldings involves evaluating the modeled structure after every monte carlo step. To find a global minimum it is necessary to have a good energy function, which can distinguish between native like structures (structures that have been already seen in solved structures and have reasonable physical and chemical interactions) and random models.
There a new amino acid environment score (buried in the core of the protein, or exposed to the solution) will be developed. An amino acids pair potential will represent favorable interactions between a pair Also a secondary structure element packing score (angle and distance between secondary structure elements) will be a part of the model evaluation. For further applications a membrane dependent energy of each function will be provided. These functions will be statistically derived from high resolution structures found in protein databanks.
Members: Nils Woetzel, Elizabeth Durham
all research projects
Ab initio modeling of protein structures using a monte carlo algorithm searching for a global minimum in the energy landscape of the possible foldings involves evaluating the modeled structure after every monte carlo step. To find a global minimum it is necessary to have a good energy function, which can distinguish between native like structures (structures that have been already seen in solved structures and have reasonable physical and chemical interactions) and random models.
There a new amino acid environment score (buried in the core of the protein, or exposed to the solution) will be developed. An amino acids pair potential will represent favorable interactions between a pair Also a secondary structure element packing score (angle and distance between secondary structure elements) will be a part of the model evaluation. For further applications a membrane dependent energy of each function will be provided. These functions will be statistically derived from high resolution structures found in protein databanks.