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Items: 1 to 20 of 119

1.

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.

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.

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.

4.

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.

5.
6.

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
7.

A quasi-physical algorithm for the structure optimization in an off-lattice protein model.

Liu JF, Huang WQ.

Genomics Proteomics Bioinformatics. 2006 Feb;4(1):61-6.

8.

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
9.

A population-based evolutionary search approach to the multiple minima problem in de novo protein structure prediction.

Saleh S, Olson B, Shehu A.

BMC Struct Biol. 2013;13 Suppl 1:S4. doi: 10.1186/1472-6807-13-S1-S4. Epub 2013 Nov 8.

10.

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
11.

A branch and bound algorithm for the protein folding problem in the HP lattice model.

Chen M, Huang WQ.

Genomics Proteomics Bioinformatics. 2005 Nov;3(4):225-30.

12.

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
13.

A replica exchange Monte Carlo algorithm for protein folding in the HP model.

Thachuk C, Shmygelska A, Hoos HH.

BMC Bioinformatics. 2007 Sep 17;8:342.

14.

A New Heuristic Algorithm for Protein Folding in the HP Model.

Traykov M, Angelov S, Yanev N.

J Comput Biol. 2016 Aug;23(8):662-8. doi: 10.1089/cmb.2016.0015. Epub 2016 May 6.

PMID:
27153764
15.

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
16.

3D protein structure prediction with genetic tabu search algorithm.

Zhang X, Wang T, Luo H, Yang JY, Deng Y, Tang J, Yang MQ.

BMC Syst Biol. 2010 May 28;4 Suppl 1:S6. doi: 10.1186/1752-0509-4-S1-S6.

17.

Extended particle swarm optimisation method for folding protein on triangular lattice.

Guo Y, Wu Z, Wang Y, Wang Y.

IET Syst Biol. 2016 Feb;10(1):30-3. doi: 10.1049/iet-syb.2015.0059.

PMID:
26816397
19.

Energy-landscape paving for prediction of face-centered-cubic hydrophobic-hydrophilic lattice model proteins.

Liu J, Song B, Liu Z, Huang W, Sun Y, Liu W.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Nov;88(5):052704. Epub 2013 Nov 6.

PMID:
24329293
20.

Guided macro-mutation in a graded energy based genetic algorithm for protein structure prediction.

Rashid MA, Iqbal S, Khatib F, Hoque MT, Sattar A.

Comput Biol Chem. 2016 Apr;61:162-77. doi: 10.1016/j.compbiolchem.2016.01.008. Epub 2016 Feb 15.

PMID:
26878130

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