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Hornak, V. and Simmerling, C., “Targeting structural flexibility in HIV-1 protease inhibitor binding”, Drug Discovery Today 12:132-138 (2007).  Link

Overview: Research in Computational Structural Biology

   The Simmerling lab at Stony Brook University carries out research in the area of computational structural biology. In particular, the lab focuses on understanding how dynamic structural changes are involved in the behavior of biomoleculs such as proteins and nucleic acids. Recent advances in computer hardware and simulation algorithms have established computational methods as a robust and important component of biomolecular research. These simulations are highly complementary to experimental tools, and methods such as molecular dynamics simulation are able to provide a detailed description of the motions of individual atoms over short timescales that are typically inaccessible to experiment. Simulations are not limited to the averages over time and over large numbers of molecules that prevent crystallographic or NMR experiments from characterizing transiently populated conformations such as important intermediates in multi-step conformational changes. In additional to direct dynamics, treatment of simulation data using statistical mechanics can provide valuable thermodynamic properties such as binding affinities or the free energy profiles resulting from conformational changes. 

    In addition to projects related to specific biological problems, much of the research in the Simmerling lab focuses on the development of new methods for biomolecular simulation. The Simmerling lab develops the Amber simulation package in collaboration with several other research groups. Of particular interest are development of new methods for efficient simulation of conformational changes and development and validation of the molecular mechanics force fields that determine the accuracy of the resulting simulation data.