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Items: 1 to 20 of 272

1.

How reliably can we predict the reliability of protein structure predictions?

Miklós I, Novák A, Dombai B, Hein J.

BMC Bioinformatics. 2008 Mar 3;9:137. doi: 10.1186/1471-2105-9-137.

2.

Stochastic pairwise alignments.

Mückstein U, Hofacker IL, Stadler PF.

Bioinformatics. 2002;18 Suppl 2:S153-60.

PMID:
12385998
3.
4.

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. doi: 10.1186/1471-2105-9-6.

5.

Accuracy of structure-based sequence alignment of automatic methods.

Kim C, Lee B.

BMC Bioinformatics. 2007 Sep 20;8:355.

6.

Vorolign--fast structural alignment using Voronoi contacts.

Birzele F, Gewehr JE, Csaba G, Zimmer R.

Bioinformatics. 2007 Jan 15;23(2):e205-11.

PMID:
17237093
7.

Multiple sequence threading: an analysis of alignment quality and stability.

Taylor WR.

J Mol Biol. 1997 Jun 27;269(5):902-43.

PMID:
9223650
8.
9.

Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints.

Lee SY, Skolnick J.

Biophys J. 2008 Aug;95(4):1956-64. doi: 10.1529/biophysj.108.129759. Epub 2008 May 16.

10.

Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information.

Ahmad S, Gromiha MM, Sarai A.

Bioinformatics. 2004 Mar 1;20(4):477-86. Epub 2004 Jan 22.

PMID:
14990443
11.

An evolutionary method for learning HMM structure: prediction of protein secondary structure.

Won KJ, Hamelryck T, Prügel-Bennett A, Krogh A.

BMC Bioinformatics. 2007 Sep 21;8:357.

12.

Partial order optimum likelihood (POOL): maximum likelihood prediction of protein active site residues using 3D Structure and sequence properties.

Tong W, Wei Y, Murga LF, Ondrechen MJ, Williams RJ.

PLoS Comput Biol. 2009 Jan;5(1):e1000266. doi: 10.1371/journal.pcbi.1000266. Epub 2009 Jan 16.

13.

I-TASSER server for protein 3D structure prediction.

Zhang Y.

BMC Bioinformatics. 2008 Jan 23;9:40. doi: 10.1186/1471-2105-9-40.

14.

Structure alignment based on coding of local geometric measures.

Chang PL, Rinne AW, Dewey TG.

BMC Bioinformatics. 2006 Jul 14;7:346.

15.

Protein fold recognition by total alignment probability.

Bienkowska JR, Yu L, Zarakhovich S, Rogers RG Jr, Smith TF.

Proteins. 2000 Aug 15;40(3):451-62.

PMID:
10861936
16.

Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions.

Huang YM, Bystroff C.

Bioinformatics. 2006 Feb 15;22(4):413-22. Epub 2005 Dec 13.

PMID:
16352653
17.

Comparative modeling without implicit sequence alignments.

Kolinski A, Gront D.

Bioinformatics. 2007 Oct 1;23(19):2522-7. Epub 2007 Jul 27.

PMID:
17660201
18.

Assessment of the probabilities for evolutionary structural changes in protein folds.

Viksna J, Gilbert D.

Bioinformatics. 2007 Apr 1;23(7):832-41. Epub 2007 Feb 4.

PMID:
17282999
19.

Consensus alignment for reliable framework prediction in homology modeling.

Prasad JC, Comeau SR, Vajda S, Camacho CJ.

Bioinformatics. 2003 Sep 1;19(13):1682-91.

PMID:
12967965
20.

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