Related papers: Lattice model of protein conformations
In the standard approach to lattice proteins the models based on nearest neighbor interaction are used. In this kind of models it is difficult to explain the existence of secondary structures --- special preferred conformations of protein…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
The precise sequence of aminoacids plays a central role in the tertiary structure of proteins and their functional properties. The Hydrophobic-Polar lattice models have provided valuable insights regarding the energy landscape. We…
Folded proteins have a modular assembly. They are constructed from regular secondary structures like alpha-helices and beta-strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe…
We present a new lattice model for proteins that incorporates a tube-like anisotropy by introducing a preference for mutually parallel alignments in the conformations. The model is demonstrated to capture many aspects of real proteins.
Protein structure is generally conceptualized as the global arrangement or of smaller, local motifs of helices, sheets, and loops. These regular, recurring secondary structural elements have well-understood and standardized definitions in…
The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
Three-dimensional protein structures usually contain regions of local order, called secondary structure, such as $\alpha$-helices and $\beta$-sheets. Secondary structure is characterized by the local rotational state of the protein…
Despite the variety of protein sizes, shapes, and backbone configurations found in nature, the design of novel protein folds remains an open problem. Within simple lattice models it has been shown that all structures are not equally…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…
Lattice-model simulations and experiments of some small proteins suggest that folding is essentially controlled by a few conserved contacts. Residues of these conserved contacts form the minimum set of native contacts needed to ensure…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Protein design is the inverse approach of the three-dimensional (3D) structure prediction for elucidating the relationship between the 3D structures and amino acid sequences. In general, the computation of the protein design involves a…
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…
A simple one-dimensional lattice model is suggested to describe the experimentally observed plateau in force-stretching diagrams for some macromolecules. This chain model involves the nearest-neighbor interaction of a Morse-like potential…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
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.…