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Easy method to predict solvent accessibility from multiple protein sequence alignments
Author(s) -
Pascarella Stefano,
De Persio Roldano,
Bossa Francesco,
Argos Patrick
Publication year - 1998
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(19980801)32:2<190::aid-prot5>3.0.co;2-p
Subject(s) - computer science , sequence (biology) , protein structure prediction , protein design , protein structure , sequence alignment , yield (engineering) , algorithm , chemistry , data mining , peptide sequence , materials science , biochemistry , metallurgy , gene
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 preference 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 through protein tertiary structural superpositions. The technique achieves the same accuracy as much more complex methods and thus provides such advantages as computational affordability, facile updating, and easily understood residue substitution patterns useful to biochemists involved in protein engineering, design, and structural prediction. The program is available from the authors; and, due to its simplicity, the algorithm can be readily implemented on any system. For a given alignment site, a hand calculation can yield a comparative prediction. Proteins 32:190–199, 1998. © 1998 Wiley‐Liss, Inc.