Related papers: Evidence for Non-Random Hydrophobicity Structures …
We present InvMSAFold, an inverse folding method for generating protein sequences that is optimized for diversity and speed. For a given structure, InvMSAFold generates the parameters of a probability distribution over the space of…
A coarse grained model of a random polypeptide chain, with only discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues is shown to display stretched exponential relaxation under Metropolis…
We analyse a simple discrete-time stochastic process for the theoretical modeling of the evolution of protein lengths. At every step of the process a new protein is produced as a modification of one of the proteins already existing and its…
We study the behavior of five proteins at the air-water and oil-water interfaces by all-atom molecular dynamics. The proteins are found to get distorted when pinned to the interface. This behavior is consistent with the phenomenological way…
Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T-P thermodynamic plane outside which the biomolecule…
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 predict analytically that diagonal correlations of amino acid positions within protein sequences statistically enhance protein propensity for nonspecific binding. We use the term 'promiscuity' to describe such nonspecific binding.…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
We consider a system consisting of a planar random walk on a square lattice, submitted to stochastic elementary local deformations. Depending on the deformation transition rates, and specifically on a parameter $\eta$ which breaks the…
Mathematical models of motility are often based on random-walk descriptions of discrete individuals that can move according to certain rules. It is usually the case that large masses concentrated in small regions of space have a great…
How typical elements that shape organisms, such as protein secondary structures, have evolved, or how evolutionarily susceptible/resistant they are to environmental changes, are significant issues in evolutionary biology, structural…
Proteins are aminoacid chains that diffusively fold or unfold depending on the thermal and chemical environmental conditions. While sophisticated models account for detailed aspects of real proteins, finding traits that unify protein…
Quantum walks exhibit many unique characteristics compared to classical random walks. In the classical setting, self-avoiding random walks have been studied as a variation on the usual classical random walk. Classical self-avoiding random…
Proteins are essential for almost all biological processes and derive their diverse functions from complex 3D structures, which are in turn determined by their amino acid sequences. In this paper, we exploit the rich biological inductive…
We study the space of all compact structures on a two-dimensional square lattice of size $N=6\times6$. Each structure is mapped onto a vector in $N$-dimensions according to a hydrophobic model. Previous work has shown that the…
We develop a simple optimization procedure for assigning binary values to the amino acids. The binary values are determined by a maximization of the degree of pattern conservation in groups of closely related protein sequences. The…
We study the conformational properties of heteropolymers containing two types of monomers A and B, modeled as self-avoiding random walks on a regular lattice. Such a model can describe in particular the sequences of hydrophobic and…
Random walks on multidimensional nonlinear landscapes are of interest in many areas of science and engineering. In particular, properties of adaptive trajectories on fitness landscapes determine population fates and thus play a central role…
Microscopic mechanisms of natural processes are frequently understood in terms of random walk models by analyzing local particle transitions. This is because these models properly account for dynamic processes at the molecular level and…
Gene expression is significantly stochastic making modeling of genetic networks challenging. We present an approximation that allows the calculation of not only the mean and variance but also the distribution of protein numbers. We assume…