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Based on large-scale Monte Carlo simulations on lattice the energy probability distribution functions are investigated for a large set of primary sequences in distinct models of copolymers at low temperatures below transitions to compacted…
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…
Native protein folds often have a high degree of symmetry. We study the relationship between the symmetries of native proteins, and their designabilities -- how many different sequences encode a given native structure. Using a…
Proteins are inherently multiscale physical systems whose functional properties emerge from coordinated structural organization across multiple spatial resolutions, ranging from atomic interactions to global fold topology. However, existing…
We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with a simple effective, coarse-grained off-lattice model to study the structure and the topology of the energy surface. The multicanonical method…
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…
The hydrophobic effect is the dominant force which drives a protein towards its native state, but its physics has not been thoroughly understood yet. We introduce an exactly solvable model of the solvation of non-polar molecules in water,…
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…
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…
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…
De novo prediction of protein folding is an open scientific challenge. Many folding models and force fields have been developed, yet all face difficulties converging to native conformations. Hydrophobicity scales (HSs) play a crucial role…
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…
We present an analytical method for determining the designability of protein structures. We apply our method to the case of two-dimensional lattice structures, and give a systematic solution for the spectrum of any structure. Using this…
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…
A simple approach is proposed to investigate the protein structure. Using a low complexity model, a simple pairwise interaction and the concept of global optimization, we are able to calculate ground states of proteins, which are in…
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…
This work addresses the question of whether it is possible to define simple pair-wise interaction terms to approximate free energies of proteins or polymers. Rather than ask how reliable a potential of mean force is, one can ask how…
A two amino acid (hydrophobic and polar) scheme is used to perform the design on target conformations corresponding to the native states of twenty single chain proteins. Strikingly, the percentage of successful identification of the nature…
On the study of protein folding, our understanding about the protein structures is limited. In this paper we find one way to characterize the compact structures of lattice protein model. A quantity called Partnum is given to each compact…
Optimization problems associated with the interaction of linked particles are at the heart of polymer science, protein folding and other important problems in the physical sciences. In this review we explain how to recast these problems as…