Prediction tables obtained for a sample text file of mutants (mutants.txt) using stability_changes_ddG.pl. For the initial run, the flag -t 0 enables the automatic retrieval of PDB files, which are saved in the main AUTO-MUTE 2.0 folder. The flag -m 0 requests that predictions (sample_output_ddG_RF.txt) be made using our previously trained random forest (RF) supervised classification model. For each requested mutant, a predicted stability category and a confidence measure (%) for the prediction are provided in the table under column headings labeled Stability and Confid., respectively. The flag -t 1 is used with the second run since the PDB files have already been downloaded, and the flag -m 2 requests that predictions (sample_output_ddG_REPTree.txt) be made using our previously trained tree regression (REPTree) model. In this case, a predicted stability change value for each requested mutant is provided in the table under the column heading labeled ddG. A glossary of terms (Glossary.txt) defining all table column headings to the right of the predictions is provided in the main folder. Briefly, parameters Vol., sT, Loc., and Num. characterize the mutated position C-alpha vertex with respect to the tessellation of the protein structure, while SS refers to the secondary structure at the mutated position, and these parameters are also discussed in Section
2.2 of the Methods. Not shown here are similar predictions based on two additional models that are available with this stability_changes_ddG.pl program: support vector machine classification (-m 1) and support vector regression (-m 3). Details for all the programs are available from the README file in the main folder, as well as by typing “perl <program_name>” without any flags at the command-line and hitting enter.
