Sequential Monte Carlo Methods in Protein Folding

• Activity Number: 105
• Type: Invited
• Date/Time: Monday, August 1, 2011 : 8:30 AM to 10:20 AM
• Sponsor: IMS
• Author(s): Samuel Kou*+
• Companies: Harvard University
• Keywords: energy function ; structure predictoin ; conditional sampling ; sequential growth ; configurational bias Monte Carlo ; protein conformation

Abstract

Predicting the native structure of a protein from its amino acid sequence is a long standing problem. A significant bottleneck of computational prediction is the lack of efficient sampling algorithms to explore of the configuration space of a protein. In this talk we will introduce a sequential Monte Carlo method to address this challenge: fragment regrowth via energy-guided sequential sampling (FRESS). The FRESS algorithm combines statistical learning (namely, learning from the protein data bank) with sequential sampling to guide the computation, resulting in a fast and effective exploration of the configurations. We will illustrate the FRESS algorithm with both lattice protein model and real proteins.