Instructions

LIST-S2 predicts the deleteriousness of amino acid mutations in proteomes. Prediction scores in the range [0 .. 1], where lower scores indicate more benign and higher indicate deleteriousness effect.

Per Mutation: To obtain LIST-S2 predictions for a list of mutations, copy and paste these mutations in the input text box and then click . Each entry should have the following format: AC:Pos:RefAA:AlleleAA

Example Input:
O08586:295:L:H
O08586:175:V:M
E1BMF7:727:Q:P
E1BMF7:727:Q:E
P07766:192:R:T
Output:
A0A0A0O08586:295:L:H	0.718928
O08586:175:V:M	0.997573
E1BMF7:727:Q:P	0.787321
E1BMF7:727:Q:E	0.929907

Per Protein: One can also visualize/download LIST-S2 scores for all possible mutations of a specific protein sequence identified by its accession number.

Enter an id value under Accession and then select:
Download: to download all scores, or
Matrix: to display an interactive matrix with all possible mutant amino acid scores color coded.
  To zoom in, use the mouse to select the region of interest, then one can zoom out by clicking [Reset zoom].

Deleteriousness

There is no ideal way to decide on a cut-off for a binary deleterious/benign decision. Since predictors are not perfect, i.e AUC is less than 1, any cut-off value is likely to leave deleterious residues identified as benign and to wrongly identify benign residues as deleterious. Therefore, we recommend that each researcher determine a cut off-value that is best suited to their tolerance of false positives/negatives. However, some users may prefer to use a generic cut-off, in this case we suggest the LIST-S2 score of 0.85 to be used as a cut-off such that mutations with a scores of 0.85 or higher to be considered as deleterious and those with a score less than 0.85 as benign.

Versions

LIST-S2: v1.10 (2020)

Species: Homo sapiens

Based on UniProt Release: 2019_10

Species: Mus musculus

Based on UniProt Release: 2019_09

Species: Sus scrofa

Based on UniProt Release: 2019_09

Species: Bos taurus

Based on UniProt Release: 2019_09

Species: Ovis aries

Based on UniProt Release: 2019_09

Species: Danio rerio

Based on UniProt Release: 2019_09

Species: Gallus gallus

Based on UniProt Release: 2019_09

Species: Primates

Based on UniProt Release: 2019_10

Species: Mammalia

Based on UniProt Release: 2019_10

Species: Vertebrata

Based on UniProt Release: 2019_10

Species: Gossypium hirsutum

Based on UniProt Release: 2020_01

Species: Glycine max

Based on UniProt Release: 2020_01

Species: Medicago sativa

Based on UniProt Release: 2020_01

Species: Solanum lycopersicum

Based on UniProt Release: 2020_01

Species: Solanum tuberosum

Based on UniProt Release: 2020_01

Species: Hordeum vulgare

Based on UniProt Release: 2020_01

Species: Oryza sativa

Based on UniProt Release: 2020_01

Species: Triticum aestivum

Based on UniProt Release: 2020_01

Species: Zea mays

Based on UniProt Release: 2020_01

Species: Zea mays subsp. mays