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Science writing skills depend on a student’s ability to co-ordinate conceptual understanding of science with the ability to articulate ideas independently, and to distinguish between gradations of importance in ideas. Real-time scaffolding of student writing during and immediately after the writing process could ease the cognitive burden of learning to co-ordinate these skills and enhance student learning of science. This paper presents a design process for automated support of real-time scaffolding of middle school students’ science explanations. We describe our adaptation of an existing tool for automatic content assessment to align more closely with a rubric, and our reliance on data mining of historical examples of middle school science writing. On a reserved test set of semi-synthetic examples of science explanations, the modified tool demonstrated high correlation with the manual rubric. We conclude the tool can support a wide range of design options for customized student feedback in real time.