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The search results for "cond-mat.dis-nn" focus on various computational approaches to studying protein folding, primarily through simplified models such as lattice models and discrete molecular dynamics. These studies explore the efficiency and theoretical underpinnings of methods like the pruned-enriched Rosenbluth method (PERM) for simulating folding processes, and investigate aspects like cooperativity and polymer diversity in folding transitions. Although these models aim to deepen understanding of protein folding, they often grapple with limitations in capturing geometrical properties and side chain diversity.
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arxiv.org
Discrete molecular dynamics studies of the folding of a protein-like model

Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical properties of the proteins (lattice models), while others are …

arxiv.org
Testing a New Monte Carlo Strategy for Folding Model Proteins

We demonstrate that the recently proposed pruned-enriched Rosenbluth method PERM (P.~Grassberger, Phys.~Rev.~{\bf E 56} (1997) 3682) leads to very efficient algorithms for the folding of simple model proteins. We test it on several models for lattice heteropolymers, and compare to published Monte …

cond-mat.soft q-bio
arxiv.org
Introducing Protein Folding Using Simple Models

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 of lattice models to understand the selection of the limited …

cond-mat.soft q-bio
arxiv.org
Remarks on homo- and hetero-polymeric aspects of protein folding

Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common approach to diversity is randomness, which is usually implemente…

cond-mat.soft cond-mat.dis-nn cond-mat.stat-mech q-bio.BM
arxiv.org
Cooperativity in Protein Folding: From Lattice Models with Side Chains to Real Proteins

We consider equilibrium folding transitions in lattice protein models with and without side chains. A dimensionless measure, $Omega_{c}$, is introduced to quantitatively assess the degree of cooperativity in lattice models and in real proteins. We show that larger values of $Ω_{c}$ resembling those…

cond-mat.soft q-bio
arxiv.org
Protein Folding Kinetics: Time Scales, Pathways, and Energy Landscapes in Terms of Sequence Dependent Properties

The folding kinetics of a number of sequences for off-lattice continuum model of proteins is studied using Langevin simulations at two values of the friction coefficient. We show that there is a remarkable correlation between folding times, $τ_{F}$, and $σ= (T_{θ} - T_{F})/T_{θ} $, where $T_{θ}…

cond-mat.stat-mech q-bio
arxiv.org
Crucial stages of protein folding through a solvable model: predicting target sites for enzyme-inhibiting drugs

An exactly solvable model based on the topology of a protein native state is applied to identify bottlenecks and key-sites for the folding of HIV-1 Protease. The predicted sites are found to correlate well with clinical data on resistance to FDA-approved drugs. It has been observed that the effects …

cond-mat.stat-mech cond-mat.soft q-bio.BM