Related papers: On correlation between protein secondary structure…
Protein secondary structure prediction (PSSP) is essential for protein function analysis. However, for low homologous proteins, the PSSP suffers from insufficient input features. In this paper, we explicitly import external self-supervised…
Proteins are translated from the N- to the C-terminus, raising the basic question of how this innate directionality affects their evolution. To explore this question, we analyze 16,200 structures from the protein data bank (PDB). We find…
We investigate the effects of alloying and growth orientation on the properties of the ultra-wide bandgap semiconductor \beta-Ga2O3 and pseudomorphic AlGaO alloy heterojunctions. Band offsets are computed from first principles using density…
In this paper, we study the structure and dynamical properties of protein contact networks with respect to other biological networks, together with simulated archetypal models acting as probes. We consider both classical topological…
The beautiful structures of single and multi-domain proteins are clearly ordered in some fashion but cannot be readily classified using group theory methods that are successfully used to describe periodic crystals. For this reason, protein…
We propose a novel approach to detect the binding between proteins making use of the anomalous diffraction of natively present heavy elements inside the molecule 3D structure. In particular, we suggest considering sulfur atoms contained in…
The correct prediction of protein secondary structures is one of the key issues in predicting the correct protein folded shape, which is used for determining gene function. Existing methods make use of amino acids properties as indices to…
$\alpha$-helices stand out as common and relatively invariant secondary structural elements of proteins. However, $\alpha$-helices are not rigid bodies and their deformations can be significant in protein function ({\it e.g.} coiled coils).…
Protein complex formation is a central problem in biology, being involved in most of the cell's processes, and essential for applications, e.g. drug design or protein engineering. We tackle rigid body protein-protein docking, i.e.,…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
Computational protein design facilitates discovery of novel proteins with prescribed structure and functionality. Exciting designs were recently reported using novel data-driven methodologies that can be roughly divided into two categories:…
Given a linear map on the vector space of symmetric matrices, every fiber intersected with the set of positive semidefinite matrices is a spectrahedron. Using the notion of the fiber body we can build the average over all such fibers and…
Phospholipids are essential building blocks of biological membranes. Despite of vast amount of accurate experimental data the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine…
In organic optoelectronics, order of conjugated molecules is required for good charge transport, but strong aggregation behavior may generate grain boundaries and trapping, opposing those benefits. Side chains on a polymer's backbone are…
The Sine Gordon theory is generalized to include several cosine terms. This is similar to the world sheet description of a string propagating in a tachyon background. This model is studied as a (boundary) 2d euclidean field theory and also…
Predicting the three-dimensional (3D) functional structures of proteins remains an important computational milestone in molecular biology to be achieved. This feat is hinged on a clear understanding of the mechanism which proteins use to…
In this work, we study whether enforcing strict compositional structure in sequence embeddings yields meaningful geometric organization when applied to protein-protein interaction networks. Using Event2Vec, an additive sequence embedding…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
The representation of protein backbone geometry through the discrete nonlinear Schr\"odinger equation provides a theoretical connection between biological structure and integrable systems. Although the global application of this framework…
Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…