The curse of the protein ribbon diagram

Abstract

Does reductionism, in the era of machine learning and now interpretable AI, facilitate or hinder scientific insight? The protein ribbon diagram, as a means of visual reductionism, is a case in point.

Fig 1. Cartoon ribbon diagrams as a blessing and a curse.

The earliest era of structural biology made clear the necessity of molecular visualization for even small proteins, such as the 62-amino acid snake venom toxin shown here (PDB ID 3EBX). In this process, (a) atomic coordinates are visually rendered on a computer display as (b) lines, “sticks,” spheres, etc., thereby creating a representation of the protein’s 3D structure. Though useful for detailed, atomic-scale analyses, e.g., of enzyme mechanisms, such renditions are too visually cluttered and complicated (incomprehensible, essentially) to enable one to grasp a protein’s overall architecture and topology. For that purpose, (c) ribbon diagrams are a blessing: these diagrams are powerful abstractions of a single protein entity, but do they (d) mask other features and relationships.