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arXiv:cs.CE/0101015v117Jan2001 A Combinatorial Toolbox for Protein Sequence Design and

Summary: arXiv:cs.CE/0101015v117Jan2001
A Combinatorial Toolbox for Protein Sequence Design and
Landscape Analysis in the Grand Canonical Model
James Aspnes
Julia Hartling
Ming-Yang Kao
Junhyong Kim§
Gauri Shah¶
June 8, 2006
In modern biology, one of the most important research problems is to understand how protein
sequences fold into their native 3D structures. To investigate this problem at a high level, one
wishes to analyze the protein landscapes, i.e., the structures of the space of all protein sequences
and their native 3D structures. Perhaps the most basic computational problem at this level is
to take a target 3D structure as input and design a fittest protein sequence with respect to one
or more fitness functions of the target 3D structure. We develop a toolbox of combinatorial
techniques for protein landscape analysis in the Grand Canonical model of Sun, Brem, Chan, and
Dill. The toolbox is based on linear programming, network flow, and a linear-size representation
of all minimum cuts of a network. It not only substantially expands the network flow technique
for protein sequence design in Kleinberg's seminal work but also is applicable to a considerably


Source: Aspnes, James - Department of Computer Science, Yale University


Collections: Computer Technologies and Information Sciences