Several course-based undergraduate research experiences (CUREs) have been published in the literature. However, only limited attempts have been made to rigorously identify the discovery-type research abilities that students actually develop during such experiences. Instead, there has been a greater focus on technical or procedural-type knowledge or general CURE skills that are too comprehensive to effectively assess. Before the extent of discovery-type learning outcomes can be established in students (termed verified learning outcomes or VLOs), it is important to rigorously identify the anticipated learning outcomes (ALOs) and to then develop student assessments that target each ALO to reveal the nature of such student learning. In this article we present a matrix of 43 ALOs, or course-based undergraduate research abilities (CURAs), that instructors anticipate students will develop during a recently-developed biochemistry CURE focusing on the prediction of protein function from structure. The CURAs were identified using the process for identifying course-based undergraduate research abilities (PICURA) and classified into seven distinct themes that enabled the characterization of the CURE and a comparison to other published inventories of research competencies and CURE aspects. These themes and the CURE protocols aligning to the CURAs were used to form the ALO matrix that was, in turn, used to inform the design of an assessment that revealed evidence that a student had developed some of the targeted CURAs. Future research will focus on further assessment development that targets other identified CURAs. This approach has potential applications to other CUREs both in biochemistry and other science disciplines. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):478-492, 2018.