Related papers: New algorithm to determine a minimal representatio…

We review algorithms for protein design in general. Although these algorithms have a rich combinatorial, geometric, and mathematical structure, they are almost never covered in computer science classes. Furthermore, many of these algorithms…

Computational methods for discovering patterns of local correlations in sequences are important in computational biology. Here we show how to determine the optimal partitioning of aligned sequences into non-overlapping segments such that…

The recent surge of utilizing deep neural networks for geometric processing and shape modeling has opened up exciting avenues. However, there is a conspicuous lack of research efforts on using powerful neural representations to extend the…

Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…

We study the structure of the set of all possible affine hyperplane sections of a convex polytope. We present two different cell decompositions of this set, induced by hyperplane arrangements. Using our decomposition, we bound the number of…

A comprehensive understanding of molecular clumps is essential for investigating star formation. We present an algorithm for molecular clump detection, called FacetClumps. This algorithm uses a morphological approach to extract signal…

Molecular interactions have widely been modelled as networks. The local wiring patterns around molecules in molecular networks are linked with their biological functions. However, networks model only pairwise interactions between molecules…

We present a new approach to 3D object representation where a neural network encodes the geometry of an object directly into the weights and biases of a second 'mapping' network. This mapping network can be used to reconstruct an object by…

Antibody-antigen interactions play a crucial role in identifying and neutralizing harmful foreign molecules. In this paper, we investigate the optimal representation for predicting the binding sites in the two molecules and emphasize the…

Wolumes is a fast and stand-alone computer program written in standard C that allows the measure of atom volumes in proteins. Its algorithm is a simple discretization of the space by means of a grid of points at 0.75 Angstroms from each…

In this work, we study and analyze different feature selection algorithms that can be used to classify cancer subtypes in case of highly varying high-dimensional data. We apply three different feature selection methods on five different…

Computational chemistry has become an important tool to predict and understand molecular properties and reactions. Even though recent years have seen a significant growth in new algorithms and computational methods that speed up quantum…

Predicting interactions between small molecules and proteins is a crucial ingredient of the drug discovery process. In particular, accurate predictive models are increasingly used to preselect potential lead compounds from large molecule…

We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…

Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…

This work proposes a multi-image matching method to estimate semantic correspondences across multiple images. In contrast to the previous methods that optimize all pairwise correspondences, the proposed method identifies and matches only a…

Model reduction of biochemical networks relies on the knowledge of slow and fast variables. We provide a geometric method, based on the Newton polytope, to identify slow variables of a biochemical network with polynomial rate functions. The…

3D fluorescence microscopy of living organisms has increasingly become an essential and powerful tool in biomedical research and diagnosis. An exploding amount of imaging data has been collected, whereas efficient and effective…

The surface of a molecule determines much of its chemical and physical property, and is of great interest and importance. In this Letter, we introduce the concept of molecular multiresolution surfaces as a new paradigm of multiscale…

Interacting particle systems play a key role in science and engineering. Access to the governing particle interaction law is fundamental for a complete understanding of such systems. However, the inherent system complexity keeps the…