Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation.

By Daniel Chasman, Rhys M. Adams. 2001

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Predicting Functional Effect of Human Missense Mutations Using PolyPhen-2 (2013, background): “It is believed that the values of B-factor of a residue may be correlated with its tolerance to amino acid substitutions (Chasman and Adams, 2001).”
Impact of selection, mutation rate and genetic drift on human genetic variation. (2003, background): “While previous analyses detected high levels of deleterious SNPs in the human population (4, 16, 29-34) here we show that selection is strong enough to prevent their fixation.”
SNAP: predict effect of non-synonymous polymorphisms on function (2007, background): “This finding confirmed results from statistical methods applied by Chasman and Adams (11).”
The amino-acid mutational spectrum of human genetic disease (2003, background): “Background Several recent studies [1-6] have applied computational methods to predict potentially deleterious effects of nonsynonymous single-nucleotide polymorphisms (SNPs) in humans.”
Human non-synonymous SNPs: server and survey. (2002, methodology): “As has been noted by Wang and Moult (9), most disease mutations and supposedly deleterious nsSNPs affect protein stability rather than functionality.”
PMUT: a web-based tool for the annotation of pathological mutations on proteins (2005, background): “Others are centered on the study of non-synonymous mutations mapped on proteins; for discussions see (Chasman and Adams, 2001; Ferrer-Costa et al., 2002, 2004, 2005; Ng and Henikoff, 2002; Saunders and Baker, 2002; Sunyaev et al., 2001; Wang and Moult, 2001).”
Evaluation of structural and evolutionary contributions to deleterious mutation prediction. (2002, background): “The entropy of a residue in a multiple sequence alignment is often used as a measure of the overall mutability of a specific site in a protein, and has appeared as a feature in previous studies of mutation prediction either directly or normalized over each protein chain.(9,11) Here, the normalized s”
Candidate-gene approaches for studying complex genetic traits: practical considerations (2002, methodology): “This approach has been used by some groups already, either by selecting only coding single-nucleotide polymorphisms (SNPs) to genotype, or by using more computational approaches to prioritizing SNPs on the basis of their predicted functional effect”