Related papers: Model of protein fragments and statistical potenti…
Lattice models, for their coarse-grained nature, are best suited for the study of the ``designability problem'', the phenomenon in which most of the about 16,000 proteins of known structure have their native conformations concentrated in a…
The biological activity and functional specificity of proteins depend on their native three-dimensional structures determined by inter- and intra-molecular interactions. In this paper, we investigate the geometrical factor of protein…
The dynamical characterization of proteins is crucial to understand protein function. From a microscopic point of view, protein dynamics is governed by the local atomic interactions that, in turn, trigger the functional conformational…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…
Spatial organisation is a hallmark of all living cells, and recreating it in model systems is a necessary step in the creation of synthetic cells. It is therefore of both fundamental and practical interest to better understand the basic…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
The idea that structural disorder might be a novel mechanism of protein interaction is widespread in the Literature, although the number of statistically significant structural studies supporting this is surprisingly low. At variance with…
We analytically derive the lower bound of the total conformational energy of a protein structure by assuming that the total conformational energy is well approximated by the sum of sequence-dependent pairwise contact energies. The condition…
Two models of binary fragmentation are introduced in which a time dependent transition size produces two regions of fragment sizes above and below the transition size. In the models we consider a fixed rate of fragmentation for the largest…
In the paper we investigate statistical and topological properties of fractional Brownian polymer chains, equipped with the short-range volume interactions. The attention is paid to statistical properties of collapsed conformations with the…
We describe the results obtained from an improved model for protein folding. We find that a good agreement with the native structure of a 46 residue long, five-letter protein segment is obtained by carefully tuning the parameters of the…
Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,''…
Nested sampling is a Bayesian sampling technique developed to explore probability distributions lo- calised in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence…
We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the…
We present a simple numerical model for investigating the general properties of fragmentation. By use of molecular dynamics simulations, we study the impact fragmentation of a solid disk of interacting particles with a wall. Regardless of…
Simple hidden Markov models are proposed for predicting secondary structure of a protein from its amino acid sequence. Since the length of protein conformation segments varies in a narrow range, we ignore the duration effect of length…
Fragment properties of hot fragmenting sources of similar sizes produced in central and semi-peripheral collisions are compared in the excitation energy range 5-10 AMeV. For semi-peripheral collisions a method for selecting compact…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…
The number of protein structures is far less than the number of sequences. By imposing simple generic features of proteins (low energy and compaction) on all possible sequences we show that the structure space is sparse compared to the…
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…