Related papers: Topological features of proteins from amino acid r…
Network measures that reflect the most salient properties of complex large-scale networks are in high demand in the network research community. In this paper we adapt a combinatorial measure of negative curvature (also called hyperbolicity)…
We develop topological methods for characterizing the relationship between polymer chain entanglement and bulk viscoelastic responses. We introduce generalized Linking Number and Writhe characteristics that are applicable to open linear…
The hydrophobic-polar (HP) model represents proteins as binary strings embedded in lattices, with fold quality measured by an energy score. We prove that the optimal fold energy is not monotonic under concatenation for several standard…
An In Silico model to relate the properties of proteins to the structure, sequence, function and evolutionary history of proteins is shown. The derived ideal sequences for amino acid residues in proteins can then be considered as attractors…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
We show that a protein can be trained to recognise multiple conformations, analogous to an associative memory, and provide capacity calculations based on energy fluctuations and information theory. Unlike the linear capacity of a Hopfield…
The similarity between protein sequences is a directly and easly computed quantity from which to deduce information about their evolutionary distance and to detect homologous proteins. The SIMAP database -- Similarity Matrix of Proteins --…
A simple lattice model for proteins that allows for distinct sizes of the amino acids is presented. The model is found to lead to a significant number of conformations that are the unique ground state of one or more sequences or encodable.…
The concept of the reduced set of contact maps is introduced. Using this concept we find the ground state candidates for Hydrophobic-Polar lattice model on a two dimensional square lattice. Using these results we exactly enumerate the…
The ability to reroute and control flow is vital to the function of venation networks across a wide range of organisms. By modifying individual edges in these networks, either by adjusting edge conductances or creating and destroying edges,…
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…
Long lived topological features are distinguished from short lived ones (considered as topological noise) in simplicial complexes constructed from complex networks. A new topological invariant, persistent homology, is determined and…
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…
Recent evidence indicates that the abundance of recurring elementary interaction patterns in complex networks, often called subgraphs or motifs, carry significant information about their function and overall organization. Yet, the…
We discuss a stochastic approach for reconstructing the native structures of proteins from the knowledge of the "effective connectivity", which is a one-dimensional structural profile constructed as a linear combination of the eigenvectors…
In this Communication we present statistical analysis of conservation profiles in families of homologous sequences for nine proteins whose folding nucleus was determined by protein engineering methods. We show that in all but one protein…
We consider a class of random, weighted networks, obtained through a redefinition of patterns in an Hopfield-like model and, by performing percolation processes, we get information about topology and resilience properties of the networks…
In this work it is shown that three pairs of the factors appear to be the key, i.e. main factors of a natural classification of protein (canonical) amino acids within the amino acid (genetic) code. First pair: the factors of the habit of an…
The adsorption of a collagen fragment on both a hydrophobic, hydrogen-terminated and a hydrophilic, natively oxidised Si surface is investigated using all-atom molecular dynamics. While favourable direct protein-surface interactions via…
Wettability of a surface depends on both surface chemistry and topography. To move a three-phase contact line, a de-pinning force needs to be applied, which is of practical importance in various applications. However, a unified…