The “Dead-End Elimination” Theorem: A New Approach to the Side-Chain Packing Problem
The prediction of a protein’s tertiary structure is still computationally infeasible, mainly because of the huge number of a priori possible global conformations. The prediction of side-chain conformations that are attached to a given, fixed main-chain structure is considered as a less complex but still important subproblem with applications to, for instance, homology modeling (Lee and Subbiah, 1991). Nevertheless, the determination of the global minimum energy conformation (GMEC) of a set of protein side chains was up to now still limited to small, densely packed units (Ponder and Richards, 1987; Lee and Levitt, 1991).
KeywordsSolvent Accessibility Accessible Surface Area Prediction Score Potential Energy Function Bovine Pancreatic Trypsin Inhibitor
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- Holm L, Sander C (1991): Database algorithm for generating protein backbone and side-chain coordinates from a C(alpha) trace. Application to model building and detection of coordinate errors. J Mol Biol 193:775–791Google Scholar
- Levinthal C (1968): Are there pathways for protein folding? J Chem Phys 65:44–45Google Scholar
- Ramanadham M, Sieker LC, Jensen LH (1989): Triclinic Lysozyme: Some Features of the Structure at 2 Angstroms Resolution, Smith-Gill S, Sercarz E, eds. Schenectady, NY: Adenine PressGoogle Scholar