This application uses the protein data bank (PDB) to acquire detailed structural information (amino acids interaction, distances between the ligand and the amino acids) about the interactions between a given ligand and its binding sites in different proteins. The program searches for and analyses all structures in the PDB containing this particular molecule to determine which amino acids are involved in binding. Searches can be specified using a number of filters including protein family, source organism and crystallographic cut-off criteria such as the resolution.
The user can determine what type of ligand they want to analyze. This allows evaluate how amino acids surround the ligand. Additionally, they can use an organism filter.
Arenas-Salinas, M., Ortega-Salazar, S., Gonzales-Nilo, F., Pohl, E., Holmes, D.S., and Quatrini, R. (2014). AFAL: a web service for profiling amino acids surrounding ligands in proteins. J. Comput. Aided. Mol. Des. (dowload)