On the computational complexity of sequence design problems
- Sandia National Labs., Albuquerque, NM (United States)
Inverse protein folding concerns the identification of an amino acid sequence that folds to a given structure. Sequence design problems attempt to avoid the apparant difficulty of inverse protein folding by defining an energy that can be minimized to find protein-like sequences. We evaluate the practical relevance of two sequence design problems by analyzing their computational complexity. We show that the canonical method of sequence design is intractable and describe approximation algorithms for this problem. We also describe an efficient algorithm that exactly solves the grand canonical method. Our analysis shows how sequence design problems can fail to reduce the difficulty of the inverse protein folding problem and highlights the need to analyze these problems to evaluate their practical relevance. 10 refs., 8 figs.
- Research Organization:
- Association for Computing Machinery, New York, NY (United States); Sloan (Alfred P.) Foundation, New York, NY (United States)
- OSTI ID:
- 549004
- Report Number(s):
- CONF-970137--
- Country of Publication:
- United States
- Language:
- English
Similar Records
Native sequence determines sidechain packing in a protein, but does optimal sidechain packing determine the native sequence?
An efficient bit string implementation of a database cross-field association system (with an application to protein sequence patterns)