Simulating Protein Structures, Complexes, And Dynamics

Computer Research And Technology

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Abstract

We continue to develop conformational searching techniques for protein structure prediction. Some encouraging results have been obtained on a model system, and a manuscript is being prepared. We have also continued to study peptide dynamics using Langevin simulations and an implicit water model. A manuscript summarizing this work is being prepared. We are about to submit another manuscript that includes the modeling of a protein implicated as a cause of the bleeding disorder Bernard-Soulier syndrome. Work continues on several collaborative efforts studying a range of biochemical systems, including dihydrofolate reductase, the human calcium receptor, and N-actyltransferase. QM/MM dynamics simulations of the proton transfer in a carbon nanotube are in progress. Molecular modeling studies on the A-beta amyloid probes are being carried out to establish a structure-activity relationship. Quantum chemical calculations are also being carried out to quantify the interaction energy between propanediol and water molecules.