2024 Coarse-grained ions for nucleic acid modeling

Coarse-grained ions for nucleic acid modeling

Author: bgtb

August undefined, 2024

WebSep 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 … 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 …

Implementation of residue-level coarse-grained models in …

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 … WebCoarse-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 … peak one shuttle breckenridge

Understanding DNA interactions in crowded environments with a coarse …

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 … WebJan 24, 2024 · Editorial: Coarse-Grained Models of Nucleic Acids and Their Applications CC BY 4.0 Authors: Maciej Maciejczyk University of Warmia and Mazury in Olsztyn … WebAug 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 … peak one surgery center colorado

Coarse-Grained Ions for Nucleic Acid Modeling - PubMed

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

WebNov 10, 2015 · A coarse grained model for the thermodynamics of nucleic acid hybridization near surfaces has been extended and parameterized to consider the contribution of … WebNov 10, 2015 · A coarse grained model for the thermodynamics of nucleic acid hybridization near surfaces has been extended and parameterized to consider the contribution of unpaired dangling ends. Theparameters of the model differ when representing a double stranded DNA section or a single stranded DNA section. lighting maintenanceWebJan 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 … peak one shuttle service

"WebCoarse-grained DNA model with rigorous effective solvent mediated potentials. Following the all-atom MD simulations of the system with four DNA molecules in all-atom representation containing explicit ions (CoHex 3+, Na +, K + and Cl −) and water as described above, we proceed to extract the effective potentials for the CG model. The ... " - Coarse-grained ions for nucleic acid modeling

Coarse-grained ions for nucleic acid modeling

Understanding DNA interactions in crowded environments with a coarse ...

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 … 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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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 … WebMar 16, 2024 · Ion Mobility Spectrometry–Mass Spectrometry (IMS-MS) is a rapidly emerging tool for the investigation of nucleic acid structure and dynamics. IMS-MS determinations can provide valuable information regarding alternative topologies, folding intermediates, and conformational heterogeneities, which are not readily accessible to …

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. … 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 ...

WebNov 4, 2024 · Nucleic acid interactions under crowded environments are of great importance for biological processes and nanotechnology. However, the kinetics and thermodynamics of nucleic acid interactions in a crowded environment remain poorly understood. We use a coarse-grained model of DNA to study the kinetic … 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 …

WebWe present a new class of coarse-grained (CG) force fields (FFs) for B-DNA with explicit ions suited for large-scale mesoscale simulations at microsecond-micrometer scale …

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 … lighting maintenance audienceWebThe diversity of available coarse-grained models for nucleic acids make it difficult to select the most appropriate for users with an average molecular-modeling background. … peak one shuttle coloradoWebApr 1, 2010 · The new coarse graining model PRIMO/PRIMONA for proteins and nucleic acids is proposed, which combines one to several heavy atoms into coarse‐grained sites that are chosen to allow an analytical, high‐resolution reconstruction of all‐atom models based on molecular bonding geometry constraints. The new coarse graining model … peak online class testsWebOct 12, 2024 · The coarse-grained model developed here can be further extended to include more interactions to mimic more complex systems, such as long-range electrostatic interactions, linear chains of particles that mimic polymeric crowders such as PEG, and be used to obtain insight into nucleic acid interactions in complex cellular environments. peak online book freeWebOct 28, 2011 · The "three sites per nucleotide" (3SPN) model provides a coarse-grained representation of nucleic acids for simulation of molecular processes. Previously, this model has relied on an implicit representation of the surrounding ionic environment at the level of Debye-Hückel theory. In this work, we el … peak online shopping hoursWebWe present a new class of coarse-grained (CG) force fields (FFs) for B-DNA with explicit ions suited for large-scale mesoscale simulations at microsecond–micrometer scale using a wide spectrum of particle simulation methods from molecular dynamics to dissipative particle dynamics. The effective solvent-mediated pairwise interactions making up the FFs are … peak one shuttle expressWebJun 17, 2014 · Coarse-Grained Ions for Nucleic Acid Modeling. Journal of Chemical Theory and Computation 2015, 11 (11) , 5436-5446. DOI: 10.1021/acs.jctc.5b00341. Aymeric Naômé, Aatto Laaksonen, and Daniel P. Vercauteren . A Coarse-Grained Simulation Study of the Structures, Energetics, and Dynamics of Linear and Circular … peak onion recall