Related papers: Amino acid classes and the protein folding problem

We use the annealed formulation of complex networks to study the dynamical behavior of disease spreading on both static and adaptive networked systems. This unifying approach relies on the annealed adjacency matrix, representing one network…

The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…

The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…

We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue -- residue contact interactions are selected based on a cutoff distance, $R_c$,…

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…

The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along…

The conformational dynamics of single-stranded nucleic acids are fundamental for nucleic acid folding and function. However, their elementary chain dynamics have been difficult to resolve experimentally. Here we employ a combination of…

We investigate the folding behavior of protein sequences by numerically studying all sequences with maximally compact lattice model through exhaustive enumeration. We get the prion-like behavior of protein folding. Individual proteins…

Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…

The local structure of a protein strongly impacts its function and interactions with other molecules. Therefore, a concise, informative representation of a local protein environment is essential for modeling and designing proteins and…

We attempt to set a mathematical foundation of immunology and amino acid chains. To measure the similarities of these chains, a kernel on strings is defined using only the sequence of the chains and a good amino acid substitution matrix…

The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family--the total number of sequences in that family--can be…

We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…

A physical scenario accounting for the existence of size-limited submicrometric domains in cell membranes is proposed. It is based on the numerical investigation of the counterpart, in lipidic membranes where proteins are diffusing, of the…

We investigated the role of peptide folding stability in peptide immunogenicity. It was the aim of this thesis to implement a stability criterion based on energy computations using an AMBER force field, and to test the implementation with a…

To confer high specificity and affinity in binding, contacts at interfaces between two interacting macromolecules are expected to exhibit pair preferences for types of atoms or residues. Here we quantify these preferences by measuring the…

The structure of a polystyrene matrix filled with tightly cross-linked polystyrene nanoparticles, forming an athermal nanocomposite system, is investigated by means of a Monte Carlo sampling formalism. The polymer chains are represented as…

Thermostability is an important prerequisite for enzymes employed for industrial applications. Several machine learning based models have thus been formulated for protein classification based on this particular trait. These models have…

Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…

Motivation: Standard algorithms for pairwise protein sequence alignment make the simplifying assumption that amino acid substitutions at neighboring sites are uncorrelated. This assumption allows implementation of fast algorithms for…