A collection of R functions to work on Evolutionary Trace (ET) related jobs.
Vignettes requires pymol to build.
remotes::install_github("LichtargeLab/EvoTrace", build_vignettes = TRUE)
To install without vignettes:
remotes::install_github("LichtargeLab/EvoTrace", build_vignettes = FALSE)
browseVignettes("EvoTrace")
ET:
- Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol. 1996 Mar 29;257(2):342-58.
- Lua RC, Wilson SJ, Konecki DM, Wilkins AD, Venner E, Morgan DH, Lichtarge O. UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures. Nucleic Acids Res. 2016 Jan 4;44(D1):D308-12.
EA:
- Katsonis P, Lichtarge O. A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness. Genome Res. 2014 Dec;24(12):2050-8.
- Wang C, Govindarajan H, Katsonis P, Lichtarge O. ShinyBioHEAT: an interactive shiny app to identify phenotype driver genes in E.coli and B.subtilis. Bioinformatics. 2023 Aug 1;39(8):btad467.
SCW Z scores: