Amino Acid Difference Formula to Help Explain Protein Evolution

By R. Grantham. 1974

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Citations in the corpus

Quantitative missense variant effect prediction using large-scale mutagenesis data (2017, positive): “Our biochemical annotations include measures of amino acid size, weight, volume, isoelectric point, and Grantham scores (Grantham, 1974).”
Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. (2004, methodology): “Ambiguously aligned regions were delimited manually (Lutzoni et al., 2000), taking into account the exchangeability of protein residues according to their chemical properties (Grantham, 1974).”
Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. (2003, methodology): “Goldman and Yang originally used the physicochemical distances of Grantham (1974), but Yang, Nielsen, and Hasegawa (1998) subsequently compared several different physicochemical distance measures and found the one of Miyata, Miyazawa, and Yasunaga (1979) to perform best.”
Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease (2003, methodology): “Although no absolute rules apply, a useful and frequently used guide is the Grantham scal”
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data (2011, unknown): “Considering non-synonymous variants, the simplest and earliest approaches to estimate deleteriousness use discrete biochemical categorizations such as ‘radical’ versus ‘conservative’ amino acid changes 32 .”
A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation (2009, methodology): “2 online) Additionally, a score for amino acid change was determined using a Grantham matri”
Capturing the mutational landscape of the beta-lactamase TEM-1 (2013, background): “At the biochemical level, the Grantham matrix (10) combining polarity composition and volume of amino acids had a performance quite similar to BLOSUMmatrices (C1 = 0.”
A survey of tools for variant analysis of next-generation genome sequencing data (2013, methodology): “SeattleSeq supplies four scores: GERP [127], Grantham [128], phastCons [129] and PolyPhen.”
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. (2002, background): “It is therefore reasonable to consider that an amino acid a is assigned to a vector whose components are the volume value v ( a ) and the polarity value p ( a ) introduced by Grantham (18).”