Related papers: Lattice model of protein conformations
We define a lattice model for the interaction of a polymer with water. We solve the model in a suitable approximation. In the case of a non-polar homopolymer, for reasonable values of the parameters, the polymer is found in a non-compact…
In this paper we introduce a novel method of deriving a pairwise potential for protein folding. The potential is obtained by optimization procedure, which simultaneously maximizes the energy gap for {\it all} proteins in the database. To…
This article reports on simulations that show how, starting with a form of neural lattice structure, it is possible to reversibly generate many alternative isomers with a lower structural symmetry, which results from twisting two hexagons…
Fundamental questions about the role of the quaternary structures are addressed using a statistical mechanics off-lattice model of a dimer protein. The model, in spite of its simplicity, captures key features of the monomer-monomer…
Hydrogen bonds are a common feature in protein folding and aggregation. Due to their chemical peculiarities in terms of strength and directionality, a particular attention must be paid to the definition of the hydrogen bond potential…
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…
New lattice model for the gradient elasticity is suggested. This lattice model gives a microstructural basis for second-order strain-gradient elasticity of continuum that is described by the linear elastic constitutive relation with the…
Hydrogen bonding is modeled in terms of virtual exchange of protons between water molecules. A simple lattice model is analyzed, using ideas and techniques from the theory of correlated electrons in metals. Reasonable parameters reproduce…
A lattice model for the study of mixtures of associating liquids is proposed. Solvent and solute are modeled by adapting the associating lattice gas (ALG) model. The nature of interaction solute/solvent is controlled by tuning the energy…
Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C$_\alpha$ carbon of a protein backbone, and for this we develop new visualization techniques to…
Lattice structures have great potential for several application fields ranging from medical and tissue engineering to aeronautical one. Their development is further speeded up by the continuing advances in additive manufacturing…
The tertiary structure of protein, as well as the local secondary structure organization are fully determined by the angles of the peptidic bound. The backbone dihedral angles not only determine the global fold of the protein, but also the…
The multiple sequence alignment (MSA) of a protein family provides a wealth of information in terms of the conservation pattern of amino acid residues not only at each alignment site but also between distant sites. In order to statistically…
Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid…
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…
Predicting protein structure from amino acid sequence is one of the most important unsolved problems of molecular biology and biophysics.Not only would a successful prediction algorithm be a tremendous advance in the understanding of the…
Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at…
Studying high-dimensional Hamiltonian systems with microstructure, it is an important and challenging problem to identify reduced macroscopic models that describe some effective dynamics on large spatial and temporal scales. This paper…