Testing the Ability of Protein-Protein Docking Programs to Model Known Complexes: A Project for the Biochemistry Classroom

Protein structure and function are important concepts in the biochemistry curriculum. A three-part CURE was developed to be used in an undergraduate biochemistry course that enhances student learning of these aspects in addition to practicing oral and written communication skills. Students used three protein-protein docking programs (PRISM, InterPred, and ZDOCK) to recreate known protein complexes and then compared the accuracy of the results of each program. This was accompanied by an individual written report and finalized by an oral group presentation to the class. The majority of feedback from students was positive, revealing that students found that the project helped them to apply the concepts learned in class and become more comfortable with scientific writing.