Usage of this web interface: The user needs to upload a complex comprising of a protein with a single chain and a ligand. The user also specifies the residue number of the ligand. This can be easily found from the PDB file. The web server runs ABS scan on the complex, assuming a default distance of 4.5 Angstroms. The web server then makes a zipped output folder available for download, which can be extracted using any standard zipping software. The file 'Alanine_Scanning_Binding_Energies_Result.csv' contains all the residue scores.
What is ABS Scan? ABS-Scan performs alanine scanning mutagenesis for a given protein-ligand complex. Binding site residues are determined through user-defined cut-off distance threshold and each of these residues are then mutated to alanine. The protein-ligand energetics is evaluated for each binding site alanine mutant generated. The protein-ligand interaction scores obtained are then compared with wild-type to evaluate the energetic contributions made by each residue in the binding site towards ligand recognition.
You can also choose to run ABS Scan as a standalone program. It is available at: https://github.com/praveeniisc/ABS-Scan
Reference #1: Anand, Praveen, et al. "ABS–Scan: in silico alanine scanning mutagenesis for binding site residues in protein–ligand complex." F1000Research 3 (2014).