Local-structural diversity and protein folding: Application to all-β off-lattice protein models

2006 ◽  
Vol 124 (2) ◽  
pp. 024905 ◽  
Author(s):  
Patricia Wang Pan ◽  
Heather L. Gordon ◽  
Stuart M. Rothstein
Keyword(s):  
Protein Folding ◽  
Structural Diversity ◽  
Protein Models ◽  
Lattice Protein Models

Monte carlo studies on equilibrium globular protein folding. II. ?-barrel globular protein models

Biopolymers ◽  
1989 ◽  
Vol 28 (6) ◽  
pp. 1059-1095 ◽  
Author(s):  
Jeffrey Skolnick ◽  
Andrzej Kolinski ◽  
Robert Yaris
Keyword(s):  
Monte Carlo ◽  
Protein Folding ◽  
Globular Protein ◽  
Monte Carlo Studies ◽  
Protein Models

Reduced Protein Models and their Application to the Protein Folding Problem

1998 ◽  
Vol 16 (2) ◽  
pp. 381-396 ◽  
Author(s):  
Jeffrey Skolnick ◽  
Andrzej Kolinski ◽  
Angel R. Ortiz
Keyword(s):  
Protein Folding ◽  
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.

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 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

COMPUTER SIMULATION OF BIOLOGICAL MACROMOLECULES IN GENERALIZED ENSEMBLES

1999 ◽  
Vol 10 (08) ◽  
pp. 1521-1530 ◽  
Author(s):  
ULRICH H. E. HANSMANN
Keyword(s):  
Computer Simulation ◽  
Protein Folding ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Biological Macromolecules ◽  
Three Dimensional Structure ◽  
Ensemble Techniques ◽  
Folding Simulations ◽  
Protein Models ◽  
Structure Of Proteins

For many years the emphasis in protein-folding simulations has been laid as to how to predict the three-dimensional structure of proteins. Only recently has there be a shift in interest towards the thermodynamics of folding. We show that generalized-ensemble techniques are well suited to study both questions for realistic protein models.

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