Coarse-grained ions for nucleic acid modeling

Author: aeqe

August undefined, 2024

WebSep 12, 2024 · Here, we introduce such a coarse-grained model that uses an Anisotropic Network Model (ANM) to represent proteins alongside the oxDNA or oxRNA model. The … WebOct 27, 2015 · The effective potentials between ions are systematically parametrized using a relative entropy coarse-graining approach [Carmichael, S. P. and M. S. Shell, J. Phys. …

A coarse-grained model for assisting the investigation of …

WebJul 2, 2024 · The three-dimensional (3D) structures of Ribonucleic acid (RNA) molecules are essential to understanding their various and important biological functions. However, experimental determination of the atomic structures is laborious and technically difficult. The large gap between the number of sequences and the experimentally determined … WebMar 31, 2015 · Most of the current docking procedures are focused on fine conformational adjustments of assembled complexes and fail to reproduce large-scale protein motion. In this paper, we test a new modeling approach developed to address this problem. CABS-dock is a versatile and efficient tool for modeling the structure, dynamics and … dog training coachella valley

Physics-driven coarse-grained model for biomolecular phase ... - Nature

WebSep 29, 2015 · We present a general coarse-grained model of sodium, magnesium, spermidine, and chlorine in implicit solvent. The effective potentials between ions are systematically parametrized using a relative entropy coarse-graining approach … WebMay 1, 2024 · The oxDNA model is a coarse-grained one-bead-per-nucleotide model of DNA with empirically derived potentials between the beads which approximate the physical, mechanical and thermodynamic properties of double- and single-stranded DNA molecules. The electrostatic repulsion between nucleotides is implemented using a Debye-Hückel … WebJan 24, 2024 · The mini-review of Li and Chan briefly describes the ideas, construction and performance of 12 models developed for the prediction of three-dimensional structure and thermodynamics of RNA. Almost all of the selected models utilize the knowledge-based approach, with the exception of oxRNA, which parametrization relies on thermodynamic … dog training clubs in roanoke va

Implementation of residue-level coarse-grained models in …

PRIMO/PRIMONA: A coarse‐grained model for proteins and nucleic acids …

WebJun 1, 2012 · Modeling nucleic acids with an all-atom representation and consequent precision is computationally expensive (Figure 1), particularly for large systems. ... we further developed our previously proposed coarse-grained model to predict 3D structure, stability, and flexibility for dsRNAs in monovalent and divalent ion solutions through … WebCoarse-grained models are widely used for molecular modeling of biomolecules [1] [2] at various granularity levels. A wide range of coarse-grained models have been proposed. … dog training club orlandoWebSep 29, 2015 · The coarse-grained, CG, parameters of the ion-ion effective potentials were obtained using relative entropy coarse-graining, RE-CG, 31 , which provides a … dog training club dallas county

"WebCoarse-grained models are widely used for molecular modeling of biomolecules at various granularity levels. A wide range of coarse-grained models have been proposed. They are usually dedicated to computational modeling of specific molecules: proteins, nucleic acids, lipid membranes, carbohydrates or water. In these models, molecules are ... " - Coarse-grained ions for nucleic acid modeling

Coarse-grained ions for nucleic acid modeling

WebMy research interest focuses on the analysis of biological complexes through molecular dynamics simulations. I have been working in the field of computational biology since 2024, and I am the first joint author in the journal Nucleic Acid Research for implementing the MERMAID web-server, developed for the preparation and running of coarse-grained … WebMar 29, 2024 · On the other hand, some CG models were developed to be easily transferrable. MARTINI, a CG model for biomolecules, was originally applied to study lipid bilayer assembly22 and later extended to proteins,23 carbohydrates,24 and nucleic acids.25,26 This model maps, generally, four heavy atoms onto one coarse-grained …

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WebTexas A&M University. Jul 2024 - Present1 year 10 months. • Development of physics based coarse grained (CG) models using experimental … WebJan 24, 2024 · In the last 10 years, one can observe also a growing number of coarse-grained models of nucleic acids, which are mostly aimed at the prediction of RNA …

WebDec 30, 2015 · In this work, we attempt to apply a coarse-grained (CG) model, which is based on anisotropic Gay–Berne and electric multipole (EMP) potentials, to the … WebOct 28, 2011 · The coarse-grain ion-ion and ion-phosphate potential energy functions are inferred from all-atom simulations and parameterized to reproduce key features of the …

WebApr 5, 2024 · Since all-atom MD simulations of large biomolecular complexes are computationally expensive, coarse-grained (CG) models based on different … WebIn this paper we study how varying oligonucleic acid backbone chemistry affects the hybridization/melting thermodynamics of oligonucleic acids. We first describe the coarse-grained (CG) model with tunable parameters that we developed to enable the study of both naturally occurring oligonucleic acids, such as DNA, and their chemically-modified ...

WebApr 4, 2024 · We present a coarse-grained molecular model of the surface of human hair, which consists of a supported lipid monolayer, in the MARTINI framework. ... work with OPLS3e to improve model accuracy on challenging regimes of drug-like chemical space that includes molecular ions and sulfur-containing moieties and introduces a novel …

WebJun 1, 2012 · Modeling nucleic acids. Nucleic acids are an important class of biological macromolecules that carry out a variety of cellular roles. For many functions, naturally occurring DNA and RNA molecules need to fold into precise three-dimensional structures. Due to their self-assembling characteristics, nucleic acids have also been widely … fairfield city council traditional ownersWebNov 10, 2015 · We present a general coarse-grained model of sodium, magnesium, spermidine, and chlorine in implicit solvent. The effective potentials between ions are … fairfield city council election 2022WebCoarse-grained models. Coarse-grained models are aimed at building simplified representations of complex systems that allow keeping the main chemical/physical peculiarities (such as the interplay between hydrophilic and hydrophobic effects) and performing affordable and meaningful simulations, which could not be feasible with, for … dog training collar sportdogWebOct 27, 2015 · We present a general coarse-grained model of sodium, magnesium, spermidine, and chlorine in implicit solvent. The effective potentials between ions are systematically parametrized using a relative entropy coarse-graining approach [Carmichael, S. P. and M. S. Shell, J. Phys. Chem. B, 116, 8383-93 (2012)] that maximizes the … dog training collar for small dogWebMar 16, 2024 · In this report, we describe the implementation of a coarse graining (CG) approach to reduce the cost of the computational methods employed in the data interpretation workflow. Our framework employs a … dog training coachingWebAug 22, 2009 · A possible way to extend molecular modeling and bridge it with experimental techniques is to use coarse-graining: to represent a system by a reduced … dog training collars for hunting dogs fairfield citizen ct