The role of chain-stiffness in lattice protein models: A replica-exchange Wang-Landau study

2018 ◽  
Vol 149 (12) ◽  
pp. 125101 ◽  
Author(s):  
Alfred C.K. Farris ◽  
Guangjie Shi ◽  
Thomas Wüst ◽  
David P. Landau
Keyword(s):  
Replica Exchange ◽  
Chain Stiffness ◽  
Protein Models ◽  
Lattice Protein Models

scholarly journals Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

2013 ◽  
Vol 14 (5) ◽  
pp. 9893-9905 ◽  
Author(s):  
Jacek Wabik ◽  
Sebastian Kmiecik ◽  
Dominik Gront ◽  
Maksim Kouza ◽  
Andrzej Koliński
Keyword(s):  
Molecular Dynamics ◽  
Coarse Grained ◽  
Replica Exchange ◽  
Protein Models

STUDIES OF FINDING LOW ENERGY CONFIGURATIONS IN OFF-LATTICE PROTEIN MODELS

2006 ◽  
Vol 05 (03) ◽  
pp. 587-594 ◽  
Author(s):  
JINGFA LIU ◽  
WENQI HUANG
Keyword(s):  
Lower Energy ◽  
Gradient Descent ◽  
Energy Landscape ◽  
Three Dimensional ◽  
Ground States ◽  
Low Energy ◽  
Protein Models ◽  
Energy Configurations ◽  
Energy Landscape Paving ◽  
Lattice Protein Models

We studied two three-dimensional off-lattice protein models with two species of monomers, hydrophobic and hydrophilic. Low energy configurations in both models were optimized using the energy landscape paving (ELP) method and subsequent gradient descent. The numerical results show that the proposed methods are very promising for finding the ground states of proteins. For all sequences with lengths 13 ≤ n ≤ 55, the algorithm finds states with lower energy than previously proposed putative ground states.

Exact methods for lattice protein models

2014 ◽  
Vol 10 (4) ◽  
Author(s):  
Martin Mann ◽  
Rolf Backofen
Keyword(s):  
Protein Structure ◽  
Structure Prediction ◽  
Prediction Method ◽  
Hydrophobic Core ◽  
Exact Methods ◽  
Optimal Structures ◽  
Energy Models ◽  
Formation And Evolution ◽  
Protein Models ◽  
Lattice Protein Models

AbstractLattice protein models are well-studied abstractions of globular proteins. By discretizing the structure space and simplifying the energy model over regular proteins, they enable detailed studies of protein structure formation and evolution. However, even in the simplest lattice protein models, the prediction of optimal structures is computationally difficult. Therefore, often, heuristic approaches are applied to find such conformations. Commonly, heuristic methods find only locally optimal solutions. Nevertheless, there exist methods that guarantee to predict globally optimal structures. Currently, only one such exact approach is publicly available, namely the constraint-based protein structure prediction method and variants. Here, we review exact approaches and derived methods. We discuss fundamental concepts like hydrophobic core construction and their use in optimal structure prediction, as well as possible applications like combinations of different energy models.

scholarly journals Computational Modelling of Glucose Uptake in the Enterocyte

Physiome ◽  
2022 ◽  
Author(s):  
Nima Afshar ◽  
Soroush Safaei ◽  
David Nickerson ◽  
Peter J. Hunter ◽  
Vinod Suresh
Keyword(s):  
Experimental Data ◽  
Glucose Transporter ◽  
Computational Modelling ◽  
Glucose Absorption ◽  
Composite Model ◽  
The Other ◽  
Sodium Glucose Cotransporter ◽  
Protein Models

We describe an implemented model of glucose absorption in the enterocyte, as previously published by Afshar et al. (2019), The model used mechanistic descriptions of all the responsible transporters and was built in the CellML framework. It was validated against published experimental data and implemented in a modular structure which allows each individual transporter to be edited independently from the other transport protein models. The composite model was then used to study the role of the sodium-glucose cotransporter (SGLT1) and the glucose transporter type 2 (GLUT2), along with the requirement for the existence of the apical Glut2 transporter, especially in the presence of high luminal glucose loads, in order to enhance the absorption. Here we demonstrate the reproduction of the figures in the original paper by using the associated model. EDITOR'S NOTE (v3): Instructions within the manuscript changed, in order to properly execute the model files. Spelling of author's name corrected in filenames. (v4): Abstract fixes.

scholarly journals Computational Modelling of Glucose Uptake in the Enterocyte

2020 ◽  
Author(s):  
Nima Afshar ◽  
Soroush Safaei ◽  
David Nickerson ◽  
Peter J. Hunter ◽  
Vinod Suresh
Keyword(s):  
Experimental Data ◽  
Glucose Transporter ◽  
Computational Modelling ◽  
Glucose Absorption ◽  
Composite Model ◽  
The Other ◽  
Sodium Glucose Cotransporter ◽  
Protein Models

We describe an implemented model of glucose absorption in the enterocyte, as previously published by Afshar et al. Afshar et al. (2019), The model used mechanistic descriptions of all the responsible transporters and was built in the CellML framework. It was validated against published experimental data and implemented in a modular structure which allows each individual transporter to be edited independently from the other transport protein models. The composite model was then used to study the role of the sodium-glucose cotransporter (SGLT1) and the glucose transporter type 2 (GLUT2), along with the requirement for the existence of the apical Glut2 transporter, especially in the presence of high luminal glucose loads, in order to enhance the absorption. Here we demonstrate the reproduction of the figures in the original paper by using the associated model.

scholarly journals Symmetry and designability for lattice protein models

2000 ◽  
Vol 113 (18) ◽  
pp. 8329-8336 ◽  
Author(s):  
Tairan Wang ◽  
Jonathan Miller ◽  
Ned S. Wingreen ◽  
Chao Tang ◽  
Ken A. Dill
Keyword(s):  
Protein Models ◽  
Lattice Protein Models

Correlation effects in parallel tempering and the role of the swapping frequency

2020 ◽  
Vol 22 (19) ◽  
pp. 10802-10806
Author(s):  
Ivano Tavernelli
Keyword(s):  
Molecular Dynamics ◽  
Parallel Tempering ◽  
Replica Exchange ◽  
Correlation Effects ◽  
Replica Exchange Molecular Dynamics ◽  
Time Frequency ◽  
Different Temperatures ◽  
Equilibrium Distributions

In this work I investigate the effect of the swapping time frequency in parallel tempering (or replica exchange molecular dynamics, REMD) on the sampled equilibrium distributions at the different temperatures.

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