ALMS stands for Automated Ligand docking with Multiple Substitutions (or something like that). An article describing ALMS is in the works. In the meantime, please take a look at the following presentations that describe the method in some detail.
Poster presentation Automating Drug Design Against Mutable Targets, with G.Moyna & W.J. Welsh, presentation at the ACS National Meeting, Anaheim, CA, MArch 1999.