SIFT

From DrugPedia: A Wikipedia for Drug discovery

SIFT, Sorting Intolerant From Tolerant, predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations.

Given a protein sequence, SIFT will return predictions for what amino acid substitutions will affect protein function.

SIFT is a multistep procedure that:

(1) searches for and chooses similar sequences

(2) makes an alignment of these sequences

(3) calculates scores based on the amino acids appearing at each position in the alignment.

SIFT is available at http://blocks.fhcrc.org/sift/SIFT.html

SIFT presumes that important amino acids will be conserved in the protein family, and so changes at well-conserved positions tend to be predicted as deleterious. For example, if a position in an alignment of a protein family only contains the amino acid isoleucine, it is presumed that substitution to any other amino acid is selected against and that isoleucine is necessary for protein function. Therefore, a change to any other amino acid will be predicted to be deleterious to protein function. If a position in an alignment contains the hydrophobic amino acids isoleucine, valine and leucine, then SIFT assumes, in effect, that this position can only contain amino acids with hydrophobic character. At this position, changes to other hydrophobic amino acids are usually predicted to be tolerated but changes to other residues (such as charged or polar) will be predicted to affect protein function.

To predict whether an amino acid substitution in a protein will affect protein function, SIFT considers the position at which the change occurred and the type of amino acid change. Given a protein sequence, SIFT chooses related proteins and obtains an alignment of these proteins with the query. Based on the amino acids appearing at each position in the alignment, SIFT calculates the probability that an amino acid at a position is tolerated conditional on the most frequent amino acid being tolerated. If this normalized value is less than a cutoff, the substitution is predicted to be deleterious.