Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions.

Abstract excerpt

We have analyzed sequence covariation in an alignment of 266 non-redundant SH3 domain sequences using chi-squared statistical methods. Artifactual covariations arising from close evolutionary relationships among certain sequence subgroups were eliminated using empirically derived sequence diversity thresholds. This covariation detection method was able to predict residue-residue contacts (side-chain centres of...

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