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An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem.

Shmygelska A, Hoos HH.

BMC Bioinformatics. 2005 Feb 14;6:30.PMID: 15710037 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 17875212 [PubMed - indexed for MEDLINE]Related articlesFree article

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 [PubMed - indexed for MEDLINE]Related articles

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 [PubMed - indexed for MEDLINE]Related articles

Search for folding nuclei in native protein structures.

Shmygelska A.

Bioinformatics. 2005 Jun;21 Suppl 1:i394-402.PMID: 15961484 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 16689690 [PubMed - indexed for MEDLINE]Related articles

Detailed protein sequence alignment based on Spectral Similarity Score (SSS).

Gupta K, Thomas D, Vidya SV, Venkatesh KV, Ramakumar S.

BMC Bioinformatics. 2005 Apr 23;6:105.PMID: 15850477 [PubMed - indexed for MEDLINE]Related articlesFree article

Exploration of two-dimensional hydrophobic-polar lattice model by combining local search with elastic net algorithm.

Guo YZ, Feng EM, Wang Y.

J Chem Phys. 2006 Oct 21;125(15):154102.PMID: 17059234 [PubMed - indexed for MEDLINE]Related articles

Evolved cellular automata for protein secondary structure prediction imitate the determinants for folding observed in nature.

Chopra P, Bender A.

In Silico Biol. 2007;7(1):87-93.PMID: 17688429 [PubMed - indexed for MEDLINE]Related articlesFree article

The elastic net algorithm and protein structure prediction.

Ball KD, Erman B, Dill KA.

J Comput Chem. 2002 Jan 15;23(1):77-83.PMID: 11913391 [PubMed - indexed for MEDLINE]Related articles

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 [PubMed - indexed for MEDLINE]Related articles

Analysis of sequence-reactivity space for protein-protein interactions.

Li J, Yi Z, Laskowski MC, Laskowski M Jr, Bailey-Kellogg C.

Proteins. 2005 Feb 15;58(3):661-71.PMID: 15624216 [PubMed - indexed for MEDLINE]Related articles

Effective optimization algorithms for fragment-assembly based protein structure prediction.

DeRonne KW, Karypis G.

Comput Syst Bioinformatics Conf. 2006:19-29.PMID: 17369622 [PubMed - indexed for MEDLINE]Related articlesFree article

Protein conformational transitions coupled to binding in molecular recognition of unstructured proteins: deciphering the effect of intermolecular interactions on computational structure prediction of the p27Kip1 protein bound to the cyclin A-cyclin-dependent kinase 2 complex.

Verkhivker GM.

Proteins. 2005 Feb 15;58(3):706-16.PMID: 15609350 [PubMed - indexed for MEDLINE]Related articles

A correlation-based method for the enhancement of scoring functions on funnel-shaped energy landscapes.

Stumpff-Kane AW, Feig M.

Proteins. 2006 Apr 1;63(1):155-64.PMID: 16397892 [PubMed - indexed for MEDLINE]Related articles

Ab-initio prediction and reliability of protein structural genomics by PROPAINOR algorithm.

Joshi RR, Jyothi S.

Comput Biol Chem. 2003 Jul;27(3):241-52.PMID: 12927100 [PubMed - indexed for MEDLINE]Related articles

Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models.

Koliński A, Bujnicki JM.

Proteins. 2005;61 Suppl 7:84-90.PMID: 16187348 [PubMed - indexed for MEDLINE]Related articles

Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study.

Klepeis JL, Wei Y, Hecht MH, Floudas CA.

Proteins. 2005 Feb 15;58(3):560-70.PMID: 15609306 [PubMed - indexed for MEDLINE]Related articles

Heuristic algorithm for off-lattice protein folding problem.

Chen M, Huang WQ.

J Zhejiang Univ Sci B. 2006 Jan;7(1):7-12.PMID: 16365919 [PubMed - indexed for MEDLINE]Related articlesFree article

Correlation between evolutionary structural development and protein folding.

Nagao C, Terada TP, Yomo T, Sasai M.

Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):18950-5. Epub 2005 Dec 19.PMID: 16365314 [PubMed - indexed for MEDLINE]Related articlesFree article