Related papers: III. Geometrical framework for thinking about glob…
Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…
We model membrane proteins as anisotropic objects characterized by symmetric-traceless tensors and determine the coupling between these order-parameters and membrane curvature. We consider the interactions between transmembrane proteins…
We investigate active particles that exhibit long-range interactions only restricted by a field of view, which is characterized by an angle $\beta$. We show that constraining attractive interactions to a field of view leads to the emergence…
Simulations of knotting and unknotting in polymers or other filaments rely on random processes to facilitate topological changes. Here we introduce a method of \textit{topological steering} to determine the optimal pathway by which a…
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 study the facial structure and Carath\'eodory number of the convex hull of an orbit of the group of rotations in R^3 acting on the space of pairs of anisotropic symmetric 3\times 3 tensors. This is motivated by the problem of determining…
Multimodal approaches that integrate protein structure and sequence have achieved remarkable success in protein-protein interface prediction. However, extending these methods to protein-peptide interactions remains challenging due to the…
Proteins constitute a large group of macromolecules with a multitude of functions for all living organisms. Proteins achieve this by adopting distinct three-dimensional structures encoded by the sequence of their constituent amino acids in…
Understanding the biological function of knots in proteins and their folding process is an open and challenging question in biology. Recent studies classify the topology and geometry of knotted proteins by analysing the distribution of a…
The paper presents a geometrical model for protein secondary structure analysis which uses only the positions of the $C_{\alpha}$-atoms. We construct a space curve connecting these positions by piecewise polynomial interpolation and…
Starting from linear chains of amino acids, the spontaneous folding of proteins into their elaborate three-dimensional structures is one of the remarkable examples of biological self-organization. We investigated native state structures of…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…
Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results indicate that short…
Analyzing the structure of proteins is a key part of understanding their functions and thus their role in biology at the molecular level. In addition, design new proteins in a methodical way is a major engineering challenge. In this work,…
The correlations of primary and secondary structures were analyzed using proteins with known structure from Protein Data Bank. The correlation values of amino acid type and the eight secondary structure types at distant position were…
The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…
We show that the contact map of the native structure of globular proteins can be reconstructed starting from the sole knowledge of the contact map's principal eigenvector, and present an exact algorithm for this purpose. Our algorithm…
Simplified Go models, where only native contacts interact favorably, have proven useful to characterize some aspects of the folding of small proteins. The success of these models is limited by the fact that all residues interact in the same…
The main chain dihedral angles play an important role to decide the protein conformation. The native states of a protein can be regard as an ensemble of a lot of similar conformations, in different conformations the main chain dihedral…
Network theorists have developed methods to characterize the complex interactions in natural phenomena. The structure of the network of interactions between proteins is important in the field of proteomics, and has been subject to intensive…