VALID AND INVALID IMPLEMENTATIONS OF GOR SECONDARY STRUCTURE PREDICTIONS

GOR algorithms have long been a standard methodology for predicting pr otein secondary structure from primary sequence. We have developed two short validation sequences for the GOR I and GOR II algorithms. Use o f these sequences with seven commercial and non-commercial implementat ions of these algorithms demonstrated that several were incorrect impl ementations, including two of the three commercial modules implementin g the GOR I algorithm. This may be due to an easy misinterpretation of the GOR I algorithm and related data tables. We present the validatio n sequences and discuss implications of this widely propagated error o n secondary and tertiary structure prediction, using several proteins of known structure in three different structural classes as examples. A valid GOR I implementation predicts secondary structure increases th e accuracy of predictions by from 1-13 percentage points over an inval id implementation based on the easy misinterpretation. A valid impleme ntation of the GOR I and GOR II algorithms is available from the autho rs.