How round is a protein? Exploring protein structures for globularity using conformal mapping.

We present a new algorithm that automatically computes a measure of the geometric difference between the surface of a protein and a round sphere. The algorithm takes as input two triangulated genus zero surfaces representing the protein and the round sphere, respectively, and constructs a discrete conformal map f between these surfaces. The conformal map is chosen to minimize a symmetric elastic energy E S (f) that measures the distance of f from an isometry. We illustrate our approach on a set of basic sample problems and then on a dataset of diverse protein structures. We show first that E S (f) is able to quantify the roundness of the Platonic solids and that for these surfaces it replicates well traditional measures of roundness such as the sphericity. We then demonstrate that the symmetric elastic energy E S (f) captures both global and local differences between two surfaces, showing that our method identifies the presence of protruding regions in protein structures and quantifies how these regions make the shape of a protein deviate from globularity. Based on these results, we show that E S (f) serves as a probe of the limits of the application of conformal mapping to parametrize protein shapes. We identify limitations of the method and discuss its extension to achieving automatic registration of protein structures based on their surface geometry

A Metric for genus-zero surfaces

We present a new method to compare the shapes of genus-zero surfaces. We introduce a measure of mutual stretching, the symmetric distortion energy, and establish the existence of a conformal diffeomorphism between any two genus-zero surfaces that minimizes this energy. We then prove that the energies of the minimizing diffeomorphisms give a metric on the space of genus-zero Riemannian surfaces. This metric and the corresponding optimal diffeomorphisms are shown to have properties that are highly desirable for applications.Comment: 33 pages, 8 figure

Neural Semantic Surface Maps

We present an automated technique for computing a map between two genus-zero shapes, which matches semantically corresponding regions to one another. Lack of annotated data prohibits direct inference of 3D semantic priors; instead, current State-of-the-art methods predominantly optimize geometric properties or require varying amounts of manual annotation. To overcome the lack of annotated training data, we distill semantic matches from pre-trained vision models: our method renders the pair of 3D shapes from multiple viewpoints; the resulting renders are then fed into an off-the-shelf image-matching method which leverages a pretrained visual model to produce feature points. This yields semantic correspondences, which can be projected back to the 3D shapes, producing a raw matching that is inaccurate and inconsistent between different viewpoints. These correspondences are refined and distilled into an inter-surface map by a dedicated optimization scheme, which promotes bijectivity and continuity of the output map. We illustrate that our approach can generate semantic surface-to-surface maps, eliminating manual annotations or any 3D training data requirement. Furthermore, it proves effective in scenarios with high semantic complexity, where objects are non-isometrically related, as well as in situations where they are nearly isometric