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Reconstructing protein structure from solvent exposure using tabu search.

Paluszewski M, Hamelryck T, Winter P.

Algorithms Mol Biol. 2006 Oct 27;1:20.PMID: 17069644 [PubMed]Related articlesFree article

HSEpred: predict half-sphere exposure from protein sequences.

Song J, Tan H, Takemoto K, Akutsu T.

Bioinformatics. 2008 Jul 1;24(13):1489-97. Epub 2008 May 8.PMID: 18467349 [PubMed - indexed for MEDLINE]Related articlesFree article

An amino acid has two sides: a new 2D measure provides a different view of solvent exposure.

Hamelryck T.

Proteins. 2005 Apr 1;59(1):38-48.PMID: 15688434 [PubMed - indexed for MEDLINE]Related articles

Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?

Taly JF, Marin A, Gibrat JF.

BMC Bioinformatics. 2008 Jan 7;9:6.PMID: 18179702 [PubMed - indexed for MEDLINE]Related articlesFree article

SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs.

Randall A, Baldi P.

BMC Struct Biol. 2008 Dec 3;8:52.PMID: 19055744 [PubMed - indexed for MEDLINE]Related articlesFree article

Design of a knowledge-based force field for off-lattice simulations of protein structure.

Liwo A, Ołdziej S, Kaźmierkiewicz R, Groth M, Czaplewski C.

Acta Biochim Pol. 1997;44(3):527-47. Review.PMID: 9511963 [PubMed - indexed for MEDLINE]Related articlesFree article

Application of tabu search strategy for finding low energy structure of protein.

Błazewicz J, Lukasiak P, Miłostan M.

Artif Intell Med. 2005 Sep-Oct;35(1-2):135-45.PMID: 16051476 [PubMed - indexed for MEDLINE]Related articles

Feature space resampling for protein conformational search.

Blum B, Jordan MI, Baker D.

Proteins. 2009 Dec 21;78(6):1583-1593. [Epub ahead of print]PMID: 20131376 [PubMed - as supplied by publisher]Related articles

An adaptive bin framework search method for a beta-sheet protein homopolymer model.

Shmygelska A, Hoos HH.

BMC Bioinformatics. 2007 Apr 24;8:136.PMID: 17451609 [PubMed - indexed for MEDLINE]Related articlesFree article

Reconstruction of 3D structures from protein contact maps.

Vassura M, Margara L, Di Lena P, Medri F, Fariselli P, Casadio R.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Jul-Sep;5(3):357-67.PMID: 18670040 [PubMed - indexed for MEDLINE]Related articles

Sequence based residue depth prediction using evolutionary information and predicted secondary structure.

Zhang H, Zhang T, Chen K, Shen S, Ruan J, Kurgan L.

BMC Bioinformatics. 2008 Sep 20;9:388.PMID: 18803867 [PubMed - indexed for MEDLINE]Related articlesFree article

Stochastic reconstruction of protein structures from effective connectivity profiles.

Wolff K, Vendruscolo M, Porto M.

PMC Biophys. 2008 Nov 26;1(1):5.PMID: 19351427 [PubMed - in process]Related articlesFree article

Search strategies in structural bioinformatics.

Oakley MT, Barthel D, Bykov Y, Garibaldi JM, Burke EK, Krasnogor N, Hirst JD.

Curr Protein Pept Sci. 2008 Jun;9(3):260-74. Review.PMID: 18537681 [PubMed - indexed for MEDLINE]Related articles

Distance matrix-based approach to protein structure prediction.

Kloczkowski A, Jernigan RL, Wu Z, Song G, Yang L, Kolinski A, Pokarowski P.

J Struct Funct Genomics. 2009 Mar;10(1):67-81. Epub 2009 Feb 18.PMID: 19224393 [PubMed - indexed for MEDLINE]Related articles

Sampling bottlenecks in de novo protein structure prediction.

Kim DE, Blum B, Bradley P, Baker D.

J Mol Biol. 2009 Oct 16;393(1):249-60. Epub 2009 Jul 28.PMID: 19646450 [PubMed - indexed for MEDLINE]Related articles

Building native protein conformation from NMR backbone chemical shifts using Monte Carlo fragment assembly.

Gong H, Shen Y, Rose GD.

Protein Sci. 2007 Aug;16(8):1515-21.PMID: 17656574 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 19003998 [PubMed - indexed for MEDLINE]Related articles

Scoring predictive models using a reduced representation of proteins: model and energy definition.

Fogolari F, Pieri L, Dovier A, Bortolussi L, Giugliarelli G, Corazza A, Esposito G, Viglino P.

BMC Struct Biol. 2007 Mar 23;7:15.PMID: 17378941 [PubMed - indexed for MEDLINE]Related articlesFree article

Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking.

Wroblewska L, Skolnick J.

J Comput Chem. 2007 Sep;28(12):2059-66.PMID: 17407093 [PubMed - indexed for MEDLINE]Related articles

Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis.

Huang YX, Bao YL, Guo SY, Wang Y, Zhou CG, Li YX.

BMC Bioinformatics. 2008 Dec 16;9:538.PMID: 19087303 [PubMed - indexed for MEDLINE]Related articlesFree article