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Updated: Aug 15, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Identification of protein folds: matching hydrophobicity patterns of sequence sets with solvent accessibility
J U Bowie1, N D Clarke, C O Pabo
1Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.
Abstract:
Hydrophobic side chains often are buried in the interior of a protein, and evolutionarily related proteins usually maintain the hydrophobic character of buried positions. In this paper we show that a pattern of hydrophobicity values derived from a set of related protein sequences is well correlated with the linear pattern of side-chain solvent accessibility values, calculated from a known protein structure representative of the sequences. In several cases, information from aligned sequences can be used to select the correct tertiary fold from a large data base of protein structures.
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