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 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.
Pascarella
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S
Dipartimento di Scienze Biochimiche e Centro di Biologia Molecolare del CNR, Università La Sapienza, Rome, Italy. pascarella@axcasp.caspur.it
De Persio
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R
Bossa
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F
Argos
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P
D000595:Amino Acid Sequence; D000596:Amino Acids; D003198:Computer Simulation; D016208:Databases, Factual; D019143:Evolution, Molecular; D037102:Lectins / Q000737:chemistry; D008969:Molecular Sequence Data; D015202:Protein Engineering; D017433:Protein Structure, Secondary; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D012984:Software; D012995:Solubility; D012997:Solvents
D000596:Amino Acids; D037102:Lectins; D012997:Solvents