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Literature DB >> 16197184

Efficient sampling of protein structures by model hopping.

Abstract

We introduce a novel simulation method, model hopping, that enhances sampling of low-energy configurations in complex systems. The approach is illustrated for a protein-folding problem. Thermodynamic quantities of proteins with up to 46 residues are evaluated from all-atom simulations with this method.

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Year: 2005 PMID： 16197184 PMCID： PMC1356668 DOI： 10.1103/PhysRevLett.95.138102

Source DB: PubMed Journal: Phys Rev Lett ISSN： 0031-9007 Impact factor: 9.161

13 in total

1. Folding of a small helical protein using hydrogen bonds and hydrophobicity forces.

Authors: Giorgio Favrin; Anders Irbäck; Stefan Wallin
Journal: Proteins Date: 2002-05-01

2. Global optimization by energy landscape paving.

Authors: Ulrich H E Hansmann; Luc T Wille
Journal: Phys Rev Lett Date: 2002-01-28 Impact factor: 9.161

3. All-atom fast protein folding simulations: the villin headpiece.

Authors: Min-yi Shen; Karl F Freed
Journal: Proteins Date: 2002-12-01

4. Parallel tempering simulations of HP-36.

Authors: Chai-Yu Lin; Chin-Kun Hu; Ulrich H E Hansmann
Journal: Proteins Date: 2003-08-15

5. An atomically detailed study of the folding pathways of protein A with the stochastic difference equation.

Authors: Avijit Ghosh; Ron Elber; Harold A Scheraga
Journal: Proc Natl Acad Sci U S A Date: 2002-07-24 Impact factor: 11.205

6. Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH.

Authors: Daniel R Ripoll; Jorge A Vila; Harold A Scheraga
Journal: J Mol Biol Date: 2004-06-11 Impact factor: 5.469

7. Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K.

Authors: J Lee; A Liwo; H A Scheraga
Journal: Proc Natl Acad Sci U S A Date: 1999-03-02 Impact factor: 11.205

8. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution.

Authors: Y Duan; P A Kollman
Journal: Science Date: 1998-10-23 Impact factor: 47.728

9. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides.

Authors: T Ooi; M Oobatake; G Némethy; H A Scheraga
Journal: Proc Natl Acad Sci U S A Date: 1987-05 Impact factor: 11.205

10. Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures.

Authors: H Gouda; H Torigoe; A Saito; M Sato; Y Arata; I Shimada
Journal: Biochemistry Date: 1992-10-13 Impact factor: 3.162

21 in total

10. Roles of boundary conditions in DNA simulations: analysis of ion distributions with the finite-difference Poisson-Boltzmann method.

Authors: Xiang Ye; Qin Cai; Wei Yang; Ray Luo
Journal: Biophys J Date: 2009-07-22 Impact factor: 4.033

Efficient sampling of protein structures by model hopping.

1. Folding of a small helical protein using hydrogen bonds and hydrophobicity forces.

2. Global optimization by energy landscape paving.

3. All-atom fast protein folding simulations: the villin headpiece.

4. Parallel tempering simulations of HP-36.

5. An atomically detailed study of the folding pathways of protein A with the stochastic difference equation.

6. Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH.

7. Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K.

8. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution.

9. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides.

10. Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures.

1. Molecular investigations into the mechanics of a muscle anchoring complex.

2. Folding of proteins with diverse folds.

3. Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent.

Review 4. Understanding protein folding: small proteins in silico.

5. Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations.

6. Simple continuous and discrete models for simulating replica exchange simulations of protein folding.

7. Optimized folding simulations of protein A.

8. Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems.

9. Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides.

10. Roles of boundary conditions in DNA simulations: analysis of ion distributions with the finite-difference Poisson-Boltzmann method.