Objectively judging the quality of a protein structure from a Ramachandran plot

Statistical methods that compare observed and expected distributions of experimental observables provide powerful tools for the quality control of protein structures. The distribution of backbone dihedral angles (‘Ramachandran plot’) has often been used for such quality control, but without a firm statistical foundation. A new and simple method is presented for judging the quality of a protein structure based on the distribution of backbone dihedral angles. Inputs to the method are 60 torsion angle distributions extracted from protein structures solved at high resolution; one for each combination of residue type and tri-state secondary structure. Output for a protein is a Ramachandran Z-score, expressing the quality of the Ramachandran plot relative to current state-of-the-art structures. The Ramachandran test is available as part of the free WHAT_CHECK program. Information about this program can be obtained on the WWW from http://swift.embl-heidelberg.de/whatcheck/ E-mail: [email protected]