Related papers: Conformations of Macromolecules and their Complexe…

Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. CryoEM provides direct visualization of individual macromolecules sampling different conformational and compositional states.…

Cryo-electron microscopy (cryo-EM) is an experimental technique for protein structure determination that images an ensemble of macromolecules in near-physiological contexts. While recent advances enable the reconstruction of dynamic…

An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…

In this paper we propose a novel algorithm to combine two or more cellular complexes, providing a minimal fragmentation of the cells of the resulting complex. We introduce here the idea of arrangement generated by a collection of cellular…

Over the past decade, advances in super-resolution microscopy and particle-based modeling have driven an intense interest in investigating spatial heterogeneity at the level of single molecules in cells. Remarkably, it is becoming clear…

Integrative modeling of macromolecular assemblies allows for structural characterization of large assemblies that are recalcitrant to direct experimental observation. A Bayesian inference approach facilitates combining data from…

Matrices are two-dimensional data structures allowing one to conceptually organize information. For example, adjacency matrices are useful to store the links of a network; correlation matrices are simple ways to arrange gene co-expression…

Single particle cryo-electron microscopy has become a critical tool in structural biology over the last decade, able to achieve atomic scale resolution in three dimensional models from hundreds of thousands of (noisy) two-dimensional…

The amount of image datasets collected for environmental monitoring purposes has increased in the past years as computer vision assisted methods have gained interest. Computer vision applications rely on high-quality datasets, making data…

Solvation is a notoriously difficult and nagging problem for the rigorous theoretical description of chemistry in the liquid phase. Successes and failures of various approaches ranging from implicit solvation modeling through dielectric…

We describe several algorithms for matrix completion and matrix approximation when only some of its entries are known. The approximation constraint can be any whose approximated solution is known for the full matrix. For low rank…

Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural…

Clustering data objects into homogeneous groups is one of the most important tasks in data mining. Spectral clustering is arguably one of the most important algorithms for clustering, as it is appealing for its theoretical soundness and is…

Clustering algorithms remain valuable tools for grouping and summarizing the most important aspects of data. Example areas where this is the case include image segmentation, dimension reduction, signals analysis, model order reduction,…

Autonomous synthesis and characterization of inorganic materials requires the automatic and accurate analysis of X-ray diffraction spectra. For this task, we designed a probabilistic deep learning algorithm to identify complex multi-phase…

Spectral clustering approaches have led to well-accepted algorithms for finding accurate clusters in a given dataset. However, their application to large-scale datasets has been hindered by computational complexity of eigenvalue…

In medical imaging, chromosome straightening plays a significant role in the pathological study of chromosomes and in the development of cytogenetic maps. Whereas different approaches exist for the straightening task, typically geometric…

Understanding complex biological macromolecules, especially proteins, is vital for grasping their diverse chemical functions with direct impact in biology and pharmacology. While techniques like X-ray crystallography and cryo-electron…

The short and intense pulses of the new X-ray free electron lasers, now operational or under construction, may make possible diffraction experiments on single molecule-sized objects with high resolution, before radiation damage destroys the…

In order to define the process of restrosynthesis of a new organic molecule, it is often necessary to be able to draw inspiration from that of a molecule similar to the target one of which we know such a process. To compute such a…