Motivation: Software in structural bioinformatics has mainly been application driven. To favor practitioners seeking off-the-shelf applications, but also developers seeking advanced building blocks to develop novel applications, we undertook the design of the Structural Bioinformatics Library ( SBL , http://sbl.inria.fr ), a generic C ++/python cross-platform software library targeting complex problems in structural bioinformatics. Its tenet is based on a modular design offering a rich and versatile framework allowing the development of novel applications requiring well specified complex operations, without compromising robustness and performances. Results: The SBL involves four software components (1-4 thereafter). For end-users, the SBL provides ready to use, state-of-the-art (1) applications to handle molecular models defined by unions of balls, to deal with molecular flexibility, to model macro-molecular assemblies. These applications can also be combined to tackle integrated analysis problems. For developers, the SBL provides a broad C ++ toolbox with modular design, involving core (2) algorithms , (3) biophysical models and (4) modules , the latter being especially suited to develop novel applications. The SBL comes with a thorough documentation consisting of user and reference manuals, and a bugzilla platform to handle community feedback. Availability and Implementation: The SBL is available from http://sbl.inria.fr. Contact: [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online.

Abstract Choosing balls that best approximate a 3D object is a non‐trivial problem. To answer it, we first address the inner approximation problem, which consists of approximating an object defined by a union of n balls with balls defining a region . This solution is further used to construct an outer approximation enclosing the initial shape, and an interpolated approximation sandwiched between the inner and outer approximations. The inner approximation problem is reduced to a geometric generalization of weighted max k‐cover, solved with the greedy strategy which achieves the classical lower bound. The outer approximation is reduced to exploiting the partition of the boundary of by the Apollonius Voronoi diagram of the balls defining the inner approximation. Implementation‐wise, we present robust software incorporating the calculation of the exact Delaunay triangulation of points with degree two algebraic coordinates, of the exact medial axis of a union of balls, and of a certified estimate of the volume of a union of balls. Application‐wise, we exhibit accurate coarse‐grain molecular models using a number of balls 20 times smaller than the number of atoms, a key requirement to simulate crowded cellular environments.

Abstract Dealing with ambiguous data is a challenge in Science in general and geometry processing in particular. One route of choice to extract information from such data consists of replacing the ambiguous input by a continuum, typically a one‐parameter family, so as to mine stable geometric and topological features within this family. This work follows this spirit and introduces a novel framework to handle 3D ambiguous geometric data which are naturally modeled by balls. First, we introduce toleranced balls to model ambiguous geometric objects. A toleranced ball consists of two concentric balls, and interpolating between their radii provides a way to explore a range of possible geometries. We propose to model an ambiguous shape by a collection of toleranced balls, and show that the aforementioned radius interpolation is tantamount to the growth process associated with an additively‐multiplicatively weighted Voronoi diagram (also called compoundly weighted or CW). Second and third, we investigate properties of the CW diagram and the associated CW α‐complex, which provides a filtration called the λ‐complex. Fourth, we sketch a naive algorithm to compute the CW VD. Finally, we use the λ‐complex to assess the quality of models of large protein assemblies, as these models inherently feature ambiguities.