The phrase "acid model for" is correct and usable in written English.
It can be used in contexts related to scientific or theoretical discussions, particularly in chemistry or modeling frameworks.
Example: "The researchers developed an acid model for predicting the behavior of chemical reactions in various environments."
Alternatives: "acid framework for" or "acid theory for".
Indeed, a researcher can build an empirical amino acid model for any taxon or clade of choice assuming there is sufficient sequence data to estimate most of the rates reliably.
The program ProtTest http://darwin.uvigo.es/software/prottest.html was used to evaluate the best amino acid model for our data from those models available in Garli.
The aligned amino acid sequences were then concatenated and imported into MEGA5 [ 21] for tree construction, with the model set to JTT (Jones-Taylor-Thornton model, the default amino acid model for MEGA5).
The Akaike information criterion (AIC; [ 68]) was used to select the best partition schemes as well as best-fit nucleotide and amino acid models for each partition.
The amino acid model of evolution used for phylogenetic inference was LG, with a discrete gamma distribution of among-site variation rates (four categories) and a proportion of invariable sites.
Bayesian analyses were performed with the parallel version of MrBayes 3.1.2 using the GTR+I+ Γ (for nucleotide) and RtREV (for amino acid) models of sequence evolution [ 86].
MrBayes was run for 5 million generations under a mixed amino acid model with a gamma correction for rate variation among sites.
We previously applied computational modeling to construct an integrated amino acid transport model for several amino acids across the human placental syncytiotrophoblast as a model epithelium (7).
Mr Bayes was allowed to estimate the best fixed rate model of protein evolution during the run by setting the prior for amino acid model to mixed.
ModelGenerator [37] was used to deduce the best-suited amino acid substitution model for the alignments.
Similar effects of SB203580 were observed in hepatocytes treated with arachidonic acid, a model for alcohol-induced liver injury [ 49].
