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Items: 1 to 20 of 164

1.

The road not taken: retreat and diverge in local search for simplified protein structure prediction.

Shatabda S, Newton MA, Rashid MA, Pham DN, Sattar A.

BMC Bioinformatics. 2013;14 Suppl 2:S19. doi: 10.1186/1471-2105-14-S2-S19. Epub 2013 Jan 21.

2.

Spiral search: a hydrophobic-core directed local search for simplified PSP on 3D FCC lattice.

Rashid MA, Newton MA, Hoque MT, Shatabda S, Pham DN, Sattar A.

BMC Bioinformatics. 2013;14 Suppl 2:S16. doi: 10.1186/1471-2105-14-S2-S16. Epub 2013 Jan 21.

3.

The simulation of the three-dimensional lattice hydrophobic-polar protein folding.

Guo YZ, Feng EM.

J Chem Phys. 2006 Dec 21;125(23):234703.

PMID:
17190566
4.
5.

An effective exact algorithm and a new upper bound for the number of contacts in the hydrophobic-polar two-dimensional lattice model.

Giaquinta E, Pozzi L.

J Comput Biol. 2013 Aug;20(8):593-609. doi: 10.1089/cmb.2012.0266.

PMID:
23899013
6.

On lattice protein structure prediction revisited.

Dotu I, Cebrián M, Van Hentenryck P, Clote P.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Nov-Dec;8(6):1620-32. doi: 10.1109/TCBB.2011.41.

PMID:
21358007
7.

Protein structure prediction with local adjust tabu search algorithm.

Lin X, Zhang X, Zhou F.

BMC Bioinformatics. 2014;15 Suppl 15:S1. doi: 10.1186/1471-2105-15-S15-S1. Epub 2014 Dec 3.

9.

Improving protein structure prediction with model-based search.

Brunette TJ, Brock O.

Bioinformatics. 2005 Jun;21 Suppl 1:i66-74.

PMID:
15961500
10.

Heuristic-based tabu search algorithm for folding two-dimensional AB off-lattice model proteins.

Liu J, Sun Y, Li G, Song B, Huang W.

Comput Biol Chem. 2013 Dec;47:142-8. doi: 10.1016/j.compbiolchem.2013.08.011. Epub 2013 Sep 8.

PMID:
24077543
11.

Scatter search algorithm for protein structure prediction.

Mansour N, Kehyayan C, Khachfe H.

Int J Bioinform Res Appl. 2009;5(5):501-15.

PMID:
19778866
12.

Enhanced hybrid search algorithm for protein structure prediction using the 3D-HP lattice model.

Zhou C, Hou C, Zhang Q, Wei X.

J Mol Model. 2013 Sep;19(9):3883-91. doi: 10.1007/s00894-013-1907-8. Epub 2013 Jul 4.

PMID:
23824509
13.

A new branch and bound method for the protein folding problem under the 2D-HP model.

Hsieh SY, Lai DW.

IEEE Trans Nanobioscience. 2011 Jun;10(2):69-75. doi: 10.1109/TNB.2011.2145388. Epub 2011 Jul 7.

PMID:
21742572
14.

Mixing energy models in genetic algorithms for on-lattice protein structure prediction.

Rashid MA, Newton MA, Hoque MT, Sattar A.

Biomed Res Int. 2013;2013:924137. doi: 10.1155/2013/924137. Epub 2013 Sep 25.

15.

A hybrid approach to protein folding problem integrating constraint programming with local search.

Ullah AD, Steinhöfel K.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S39. doi: 10.1186/1471-2105-11-S1-S39.

16.

Optimal HP configurations of proteins by combining local search with elastic net algorithm.

Guo YZ, Feng EM, Wang Y.

J Biochem Biophys Methods. 2007 Apr 10;70(3):335-40. Epub 2006 Aug 9.

PMID:
16982100
17.
18.
19.

Accurate prediction for atomic-level protein design and its application in diversifying the near-optimal sequence space.

Fromer M, Yanover C.

Proteins. 2009 May 15;75(3):682-705. doi: 10.1002/prot.22280.

PMID:
19003998
20.

Protein folding in hydrophobic-polar lattice model: a flexible ant-colony optimization approach.

Hu XM, Zhang J, Xiao J, Li Y.

Protein Pept Lett. 2008;15(5):469-77.

PMID:
18537736

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