Related papers: Structural Determinant of Protein Designability
In previous works it was shown that protein 3D-conformations could be encoded into discrete sequences called dominance partition sequences (DPS), that generated a linear partition of molecular conformational space into regions of molecular…
Lattice protein models, as the Hydrophobic-Polar (HP) model, are a common abstraction to enable exhaustive studies on structure, function, or evolution of proteins. A main issue is the high number of optimal structures, resulting from the…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…
By enumerating all sequences of length 20, we study the designability of structures in a two-dimensional Hydrophobic-Polar (HP) lattice model in a wide range of inter-monomer interaction parameters. We find that although the histogram of…
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…
An effective potential function is critical for protein structure prediction and folding simulation. For simplified models of proteins where coordinates of only $C_\alpha$ atoms need to be specified, an accurate potential function is…
Monte Carlo simulations of a simple lattice model of protein folding show two distinct regimes depending on the chain length. The first regime well describes the folding of small protein sequences and its kinetic counterpart appears to be…
The simplest approximation of interaction potential between amino-acids in proteins is the contact potential, which defines the effective free energy of a protein conformation by a set of amino acid contacts formed in this conformation.…
The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…
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…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
Structure determination is key to understanding protein function at a molecular level. Whilst significant advances have been made in predicting structure and function from amino acid sequence, researchers must still rely on expensive,…
In this letter, the possible dynamic scaling properties of protein molecules in folding are investigated theoretically by assuming that the protein molecules are percolated networks. It is shown that the fractal character and the fractal…
We investigate the extent to which the commonly used standard pairwise contact potential can be used to identify the native fold of a protein. Ideally one would hope that a universal energy function exists, for which the native folds of all…
A method to reconstruct the energy landscape of small peptides is presented with reference to a 2d off--lattice model. The starting point is a statistical analysis of the configurational distances between generic minima and directly…
The molecular distributions obtained from canonical Monte Carlo simulations can be used to find an approximate interaction energy. This serves as the basis of a method for estimating the binding free energy for a ligand to a protein which…
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…
An effective potential function is critical for protein structure prediction and folding simulation. Simplified protein models such as those requiring only $C_\alpha$ or backbone atoms are attractive because they enable efficient search of…
Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show…
The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum…