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. 2018 Summer;17(2):es4. doi: 10.1187/cbe.17-12-0250

TABLE 6.

Example of data yielded by Step 2 of PICURA: Open-ended survey

Selected questions from the surveya Analysis → Output: coded responses from the lead designera
Q: Explain how you, or other scientists, use computational work and protein structural data to investigate protein function. Once all the participants (instructors and designers) had completed the open-ended survey, the responses were analyzed for the concepts and representations (bolded), as well as, the reasoning (italicized) applied.b Additionally, participant responses and the level of detail they provided were recorded. A: 1. Look for structural alignments of the full protein backboneto identify folds or families RM. 2. Look for template based alignments of small motifsto identify active sites or ligand binding sitesRM. 3. Look at sequence alignments (BLAST)to identify protein familiesRM. 4. Explore Pfam and UniProt to study the families. 5. Identify ligands that bind [substrate binding] to members of these protein familiesRC. 6. Dock the ligands to the proteins and see [determine] if there are favorable binding energiesRM.
Q: Please list and describe the types of representations you use, and how you use them, when thinking about or explaining protein function. A: 1. Enzyme assays: chemical reaction drawings help us to understandhow the parts of a protein catalyze a ­reactionRM. 2. Molecular visualization: ligand bindingdemonstrates if a substrate binds to an active siteRC [e.g., a LigPlot+ figure was provided and is shown in Figure 2B].
Output: general observations

  • Participants tended to discuss items in sequential order, often similar to how they are presented to the students.

  • Though reasoning elements were identified, they were at a basal level.

aFull set of survey questions and responses for the lead designer is provided in the Supplemental Material.

bUnderlining indicates either an RM or RC (superscript) coded segment with verbs (italics) showing reasoning associated with the noun (bold), which is either a concept or representation.