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Items: 1 to 20 of 147

1.

Generalized simulated annealing applied to protein folding studies.

Agostini FP, Soares-Pinto Dde O, Moret MA, Osthoff C, Pascutti PG.

J Comput Chem. 2006 Aug;27(11):1142-55.

PMID:
16732545
3.

Simulated annealing coupled replica exchange molecular dynamics--an efficient conformational sampling method.

Kannan S, Zacharias M.

J Struct Biol. 2009 Jun;166(3):288-94. doi: 10.1016/j.jsb.2009.02.015. Epub 2009 Mar 9.

PMID:
19272454
4.

GSAFold: a new application of GSA to protein structure prediction.

Melo MC, Bernardi RC, Fernandes TV, Pascutti PG.

Proteins. 2012 Aug;80(9):2305-10. doi: 10.1002/prot.24120. Epub 2012 Jun 18.

PMID:
22622959
5.

Generalized-ensemble algorithms for molecular simulations of biopolymers.

Mitsutake A, Sugita Y, Okamoto Y.

Biopolymers. 2001;60(2):96-123. Review.

PMID:
11455545
6.

Simulated Q-annealing: conformational search with an effective potential.

Son WJ, Jang S, Shin S.

J Mol Model. 2012 Jan;18(1):213-20. doi: 10.1007/s00894-011-1072-x. Epub 2011 Apr 27.

PMID:
21523533
7.
8.

Applications of simulated annealing to peptides.

Wilson SR, Cui WL.

Biopolymers. 1990 Jan;29(1):225-35.

PMID:
2328288
9.

Comparative study of generalized born models: Born radii and peptide folding.

Zhu J, Alexov E, Honig B.

J Phys Chem B. 2005 Feb 24;109(7):3008-22.

PMID:
16851315
10.

Computational study of the conformational domains of peptide T.

Filizola M, Centeno NB, Perez JJ.

J Pept Sci. 1997 Mar-Apr;3(2):85-92.

PMID:
9230473
11.

Flexibility of "polyunsaturated fatty acid chains" and peptide backbones: A comparative ab initio study.

Law JM, Setiadi DH, Chass GA, Csizmadia IG, Viskolcz B.

J Phys Chem A. 2005 Jan 27;109(3):520-33.

PMID:
16833374
12.

Stochastic protein folding simulation in the three-dimensional HP-model.

Albrecht AA, Skaliotis A, Steinhöfel K.

Comput Biol Chem. 2008 Aug;32(4):248-55. doi: 10.1016/j.compbiolchem.2008.03.004. Epub 2008 Mar 26.

PMID:
18485827
13.

A minima hopping study of all-atom protein folding and structure prediction.

Roy S, Goedecker S, Field MJ, Penev E.

J Phys Chem B. 2009 May 21;113(20):7315-21. doi: 10.1021/jp8106793.

PMID:
19391598
14.

Conformational equilibrium in alanine-rich peptides probed by reversible stretching simulations.

Hénin J, Schulten K, Chipot C.

J Phys Chem B. 2006 Aug 24;110(33):16718-23.

PMID:
16913811
15.

Exploring the free-energy landscape of a short peptide using an average force.

Chipot C, Hénin J.

J Chem Phys. 2005 Dec 22;123(24):244906.

PMID:
16396572
16.

Population-based local search for protein folding simulation in the MJ energy model and cubic lattices.

Kapsokalivas L, Gan X, Albrecht AA, Steinhöfel K.

Comput Biol Chem. 2009 Aug;33(4):283-94. doi: 10.1016/j.compbiolchem.2009.06.006. Epub 2009 Jul 3.

PMID:
19647489
17.

Evaluation of a grid based molecular dynamics approach for polypeptide simulations.

Merelli I, Morra G, Milanesi L.

IEEE Trans Nanobioscience. 2007 Sep;6(3):229-34.

PMID:
17926781
18.
19.

Extensive exploration of conformational space improves Rosetta results for short protein domains.

Li Y, Bordner AJ, Tian Y, Tao X, Gorin AA.

Comput Syst Bioinformatics Conf. 2008;7:203-9.

20.

ARTIST: an activated method in internal coordinate space for sampling protein energy landscapes.

Yun MR, Lavery R, Mousseau N, Zakrzewska K, Derreumaux P.

Proteins. 2006 Jun 1;63(4):967-75.

PMID:
16523485
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