Alberto Perez, University of Florida

Modeling molecular recognition in flexible systems

Speaker: Alberto Perez, University of Florida

Host: Pratyush Tiwary

Abstract: 

Most macromolecules interact with other molecules in order to carry out their biological role. By understanding the structures of complexes, the different binding modes and the interactions that drive binding, we can design new molecules that promote or inhibit proteins. Computational modeling has played a significant role in predicting and identifying small molecule binding through techniques such as docking and alchemical free energy calculations. However, the success rate with flexible molecules is much lower. 

In this talk, I will present two directions in our efforts to combine information and simulations to predict the structures of complexes involving conformational changes. In the first example, we predict the structures of intrinsically disordered peptides that fold upon binding the extra terminal domain of bromo and extra terminal domain proteins – a class of proteins involved in cancer and viral infection. In the second example, I will present our work to predict protein-nucleic acid complexes using generic information and our MELD simulation framework.

Seminars start at 4:00 pm, and refreshments will be served at 3:45 pm. All seminars are held in the Conference Room (1116) of the Institute for Physical Science and Technology (IPST) Building (Bldg #085) unless otherwise noted.