TCBG Seminar

Studying biomolecular dynamics using structure-based potentials with SMOG

Dr. Jeff Noel
University of Texas at Austin
Austin, Texas

Monday, August 13, 2012
3:00 pm (CT)
3269 Beckman Institute


The energy landscape theory of biomolecular folding is the theoretical underpinning of structure-based models, models that introduce a native bias by explicitly including structural information in the Hamiltonian. These models have been successful in describing protein folding and in recent years have been pushed towards studying the folding of RNA and conformational transitions in proteins, RNA, and molecular machines. I will introduce our breed of structure-based models, which are typically perfect funnel models. A hope is to fully implement these potentials efficiently in NAMD. As motivation, I will discuss applications to the folding of proteins with complex topologies and accommodation of tRNA into the ribosome.

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