338 research outputs found
An Analytical Approach to the Protein Designability Problem
We present an analytical method for determining the designability of protein
structures. We apply our method to the case of two-dimensional lattice
structures, and give a systematic solution for the spectrum of any structure.
Using this spectrum, the designability of a structure can be estimated. We
outline a heirarchy of structures, from most to least designable, and show that
this heirarchy depends on the potential that is used.Comment: 16 pages 4 figure
A New Algorithm for Protein Design
We apply a new approach to the reverse protein folding problem. Our method
uses a minimization function in the design process which is different from the
energy function used for folding. For a lattice model, we show that this new
approach produces sequences that are likely to fold into desired structures.
Our method is a significant improvement over previous attempts which used the
energy function for designing sequences.Comment: 10 pages latex 2.09 no figures. Use uufiles to decod
Protein design: A perspective from simple tractable models
We review the recent progress in computational approaches to protein design
which builds on advances in statistical-mechanical protein folding theory. In
particular, we evaluate the degeneracy of the protein code (i.e. how many
sequences fold into a given conformation) and outline a simple condition for
''designability`` in a protein model. From this point of view we discuss
several popular protein models that were used for sequence design by several
authors. We evaluate the strengths and weaknesses of popular approaches based
on stochastic optimization in sequence space and discuss possible ways to
improve them to bring them closer to experiment. We also discuss how sequence
design affects folding and point out to some features of proteins that can be
deigned ''in'' or designed ''out''}Comment: 12 pages three figure
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