Related papers: Enumerating Designing Sequences in the HP Model
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
Among the unsolved problems in computational biology, protein folding is one of the most interesting challenges. To study this folding, tools like neural networks and genetic algorithms have received a lot of attention, mainly due to the…
We fit the Fourier transforms of solvent accessibility and hydrophobicity profiles of a representative set of proteins to a joint multi-variable Gaussian. This allows us to separate the intrinsic tendencies of sequence and structure…
The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling. Three benchmark HP sequences (48mer, 67mer, and 103mer) are…
We study the phase behavior of single homopolymers in a simple hydrophobic/hydrophilic off-lattice model with sequence independent local interactions. The specific heat is, not unexpectedly, found to exhibit a pronounced peak well below the…
With the aim to study the relationship between protein sequences and their native structures, we adopt vectorial representations for both sequence and structure. The structural representation is based on the Principal Eigenvector of the…
Planar/flat configurations of fixed-angle chains and trees are well studied in the context of polymer science, molecular biology, and puzzles. In this paper, we focus on a simple type of fixed-angle linkage: every edge has unit length…
We study a single statistical amphiphilic copolymer chain AB in a selective solvent (e.g.water). Two situations are considered. In the annealed case, hydrophilic (A) and hydrophobic (B) monomers are at local chemical equilibrium and both…
Applying multicanonical simulations we investigated folding properties of off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing…
We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our…
The density of states contains all informations on energetic quantities of a statistical system, such as the mean energy, free energy, entropy, and specific heat. As a specific application, we consider in this work a simple lattice model…
We consider a two-letter self-avoiding (square) lattice heteropolymer model of N_H (out ofN) attracting sites. At zero temperature, permanent links are formed leading to collapse structures for any fraction rho_H=N_H/N. The average chain…
Histogram-reweighting grand canonical Monte Carlo simulations are used to obtain the critical properties of lattice chains composed of solvophilic and solvophobic monomers. The model is a modification of one proposed by Larson \emph{et al.}…
Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical…
We study the behaviour of a hydrophobic chain near a hydrophobic boundary in two dimensions, using the decorated lattice model of Berkema and Widom [G.T. Barkema and B. Widom, J. Chem. Phys. 113, 2349 (2000)] to obtain effective,…
We present an exact enumeration algorithm for identifying the {\it native} configuration - a maximally compact self avoiding walk configuration that is also the minimum energy configuration for a given set of contact-energy schemes; the…
The combination of two techniques (Small Angle X-ray Scattering and Atomic Force Microscopy) has allowed us to measure in reciprocal and real space the correlation length $\xi$ of salt-free aqueous solutions of highly charged hydrophobic…
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…
Evolutionally conserved quantity that specifies folding nuclei is pursued by a case study for a small protein (PDB code: 1ten). First it is demonstrated that the sequences of amino acids at folding nuclei are not conserved. Then 3D…
We study a single self avoiding hydrophilic hydrophobic polymer chain, through Monte Carlo lattice simulations. The affinity of monomer $i$ for water is characterized by a (scalar) charge $\lambda_{i}$, and the monomer-water interaction is…