EASY METHOD TO PREDICT SOLVENT ACCESSIBILITY FROM MULTIPLE PROTEIN-SEQUENCE ALIGNMENTS

An easy and uncomplicated method to predict the solvent accessibility state of a site in a multiple protein sequence alignment is described. The approach is based on amino acid exchange and compositional prefer ence matrices for each of three accessibility states: buried, exposed, and intermediate, Calculations utilized a modified version of the 3D_ ali databank, a collection of multiple sequence alignments anchored th rough protein tertiary structural superpositions. The technique achiev es the same accuracy as much more complex methods and thus provides su ch advantages as computational affordability, facile updating, and eas ily understood residue substitution patterns useful to biochemists inv olved in protein engineering, design, and structural prediction. The p rogram is available from the authors; and, due to its simplicity, the algorithm can be readily implemented on any system. For a given alignm ent site, a hand calculation can yield a comparative prediction. Prote ins 32:190-199, 1998. (C) 1998 Wiley-Liss, Inc.