RUTCOR Colloquia - November 4, 2004
Speaker: Yuval Nov
Affiliation: Stanford University
Title: Modeling and Analysis of Protein Design under Resource Constraints
Time: 1:30 - 2:30 PM
Location: RUTCOR Building - Room 139, Rutgers University, Busch Campus,
Piscataway, NJ
Abstract: The potency, or fitness, of a protein-based drug can be
enhanced by changing the sequence of its underlying protein. We present a novel
stochastic model for the sequence--fitness relation, and estimate its parameters
from industrial data. Using this model, we formulate, analyze, and solve two
variants of the protein design problem. In the single-period design problem,
the designer needs to decide under capacity constraints which set of sequences
to screen in order to maximize the expected fitness of the best sequence in the
set. In the more general two-period design problem, the designer can afford two
screening rounds, and needs to allocate resources optimally across the two
periods to maximize the same objective function. Analytical and simulation
results allow us to identify promising design strategies for various parameter
regimes.
Joint work with Prof. Larry Wein.
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