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Look‐up tables for protein solvent accessibility prediction and nearest neighbor effect analysis
Author(s) -
Wang JungYing,
Ahmad Shandar,
Gromiha M. Michael,
Sarai Akinori
Publication year - 2004
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.20113
Subject(s) - solvent , chemistry , amino acid residue , residue (chemistry) , accessible surface area , k nearest neighbors algorithm , table (database) , computational chemistry , computer science , organic chemistry , peptide sequence , biochemistry , data mining , artificial intelligence , gene
Abstract We developed dictionaries of two‐, three‐, and five‐residue patterns in proteins and computed the average solvent accessibility of the central residues in their native proteins. These dictionaries serve as a look‐up table for making subsequent predictions of solvent accessibility of amino acid residues. We find that predictions made in this way are very close to those made using more sophisticated methods of solvent accessibility prediction. We also analyzed the effect of immediate neighbors on the solvent accessibility of residues. This helps us in understanding how the same residue type may have different accessible surface areas in different proteins and in different positions of the same protein. We observe that certain residues have a tendency to increase or decrease the solvent accessibility of their neighboring residues in C‐ or N‐terminal positions. Interestingly, the C‐terminal and N‐terminal neighbor residues are found to have asymmetric roles in modifying solvent accessibility of residues. As expected, similar neighbors enhance the hydrophobic or hydrophilic character of residues. Detailed look‐up tables are provided on the web at www.netasa.org/look‐up/ . © 2004 Wiley Periodicals, Inc. Biopolymers, 2004