A short example of what I am trying to accomplish:

Starting String: VSC

Potential AA substitutions:\ V to L/A\ S to T\ C to M

Output:ASC,LSC,ATC,LTC,ATM,LTM,VSM,VTM .... and other potential matches

I have thought about using expand.grid or another similar function, but I need more specificity for these substitutions. Ex: S should not be substituted for M.

Sorry for the slow response, I was on vacation.

As far as I'm aware, there isn't a function to do this in Biostrings, but it should be pretty simple to do on your own using expand.grid and a lookup table. For example, using your inputs:

make_possible_subs <- function(aa,mapping){
    split_val <- strsplit(aa, '')[[1]]
    expand.grid(mapping[split_val]) |> apply(1L, paste, collapse='')
}

test <- "VSC"

lookup_map <- list(
    V=c("V","L","A"),
    S=c("S","T"),
    C=c("C","M")
)
make_possible_subs(test, lookup_map)

## Output:
## [1] "VSC" "LSC" "ASC" "VTC" "LTC" "ATC" "VSM" "LSM" "ASM" "VTM" "LTM" "ATM"

If you need it as an AAString, you could just pipe the apply call to AAStringSet at the end.

Does that solution accomplish what you're looking for, or are there other restrictions to the problem that make this approach infeasible?