Related papers: Lattice model of protein conformations
Understanding the mechanism of protein secondary structure formation is an essential part of protein-folding puzzle. Here we describe a simple model for the formation of the $\beta$-hairpin, motivated by the fact that folding of a…
We discuss a model of protein conformations where the conformations are combinations of short fragments from some small set. For these fragments we consider a distribution of frequencies of occurrence of pairs (sequence of amino acids,…
A rigourous Monte Carlo method for protein folding simulation on lattice model is introduced. We show that a parameter which can be seen as the rigidity of the conformations has to be introduced in order to satisfy the detailed balance…
We investigate a lattice-fluid model of water, defined on a three-dimensional body centered cubic lattice. Model molecules possess a tetrahedral symmetry, with four equivalent bonding arms, aiming to mimic the formation of hydrogen bonds.…
Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
We propose that protein loops can be interpreted as topological domain-wall solitons. They interpolate between ground states that are the secondary structures like alpha-helices and beta-strands. Entire proteins can then be folded simply by…
We construct a three-dimensional lattice model for biological gels in which straight lines of bonds correspond to filamentous semi-flexible polymers and lattice sites, which are exactly four-fold coordinated, to crosslinks. With only…
Using a fast tree-searching algorithm and a Pentium cluster, we enumerated all the sequences and compact conformations (structures) for a protein folding model on a cubic lattice of size $4\times3\times3$. We used two types of amino acids…
In this work we introduce a new semi-implicit second order correction scheme to the kinetic Kohn-Sham lattice model. The new approach is validated by performing realistic exchange-correlation energy calculations of atoms and dimers of the…
We propose an energy-based model (EBM) of protein conformations that operates at atomic scale. The model is trained solely on crystallized protein data. By contrast, existing approaches for scoring conformations use energy functions that…
A new method for the Automated Protein Structure Analysis (APSA) is derived, which simplifies the protein backbone to a smooth curve in 3-dimensional space. For the purpose of obtaining this smooth line each amino acid is represented by its…
Lattice models for the second-order strain-gradient models of elasticity theory are discussed. To combine the advantageous properties of two classes of second-gradient models, we suggest a new lattice model that can be considered as a…
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…
Proteins in photosynthetic membranes can organize into patterned arrays that span the membrane's lateral size. Attractions between proteins in different layers of a membrane stack can play a key role in this ordering, as was suggested by…
A typical protein structure is a compact packing of connected alpha-helices and/or beta-strands. We have developed a method for generating the ensemble of compact structures a given set of helices and strands can form. The method is tested…
The simulation of a protein's folding process is often done via stochastic local search, which requires a procedure to apply structural changes onto a given conformation. Here, we introduce a constraint-based approach to enumerate lattice…
A two-dimensional square-lattice model for the formation of secondary structures in proteins, the hydrogen-bonding model, is extended to include the effects of solvent quality. This is achieved by allowing configuration-dependent…
We have investigated the potential energy surface for neutral and charged alanine and glycine chains consisting of up to 6 amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran…