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Items: 1 to 20 of 84

1.

Building and assessing atomic models of proteins from structural templates: learning and benchmarks.

Vallat BK, Pillardy J, Májek P, Meller J, Blom T, Cao B, Elber R.

Proteins. 2009 Sep;76(4):930-45. doi: 10.1002/prot.22401.

2.

A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins.

Vallat BK, Pillardy J, Elber R.

Proteins. 2008 Aug 15;72(3):910-28. doi: 10.1002/prot.21976.

3.

Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling.

Meier A, Söding J.

PLoS Comput Biol. 2015 Oct 23;11(10):e1004343. doi: 10.1371/journal.pcbi.1004343. eCollection 2015 Oct.

4.

A multi-template combination algorithm for protein comparative modeling.

Cheng J.

BMC Struct Biol. 2008 Mar 17;8:18. doi: 10.1186/1472-6807-8-18.

5.

Increased detection of structural templates using alignments of designed sequences.

Larson SM, Garg A, Desjarlais JR, Pande VS.

Proteins. 2003 May 15;51(3):390-6.

PMID:
12696050
6.

Automated structure prediction of weakly homologous proteins on a genomic scale.

Zhang Y, Skolnick J.

Proc Natl Acad Sci U S A. 2004 May 18;101(20):7594-9. Epub 2004 May 4.

7.

I-TASSER: fully automated protein structure prediction in CASP8.

Zhang Y.

Proteins. 2009;77 Suppl 9:100-13. doi: 10.1002/prot.22588.

8.

Prediction of protein-protein interaction sites from weakly homologous template structures using meta-threading and machine learning.

Maheshwari S, Brylinski M.

J Mol Recognit. 2015 Jan;28(1):35-48. doi: 10.1002/jmr.2410.

PMID:
26268369
9.

M4T: a comparative protein structure modeling server.

Fernandez-Fuentes N, Madrid-Aliste CJ, Rai BK, Fajardo JE, Fiser A.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W363-8. Epub 2007 May 21.

10.

De novo and inverse folding predictions of protein structure and dynamics.

Godzik A, Kolinski A, Skolnick J.

J Comput Aided Mol Des. 1993 Aug;7(4):397-438. Review.

PMID:
8229093
11.

Fold recognition by predicted alignment accuracy.

Xu J.

IEEE/ACM Trans Comput Biol Bioinform. 2005 Apr-Jun;2(2):157-65.

PMID:
17044180
12.

RAPTOR: optimal protein threading by linear programming.

Xu J, Li M, Kim D, Xu Y.

J Bioinform Comput Biol. 2003 Apr;1(1):95-117.

PMID:
15290783
13.

A guide to template based structure prediction.

Qu X, Swanson R, Day R, Tsai J.

Curr Protein Pept Sci. 2009 Jun;10(3):270-85. Review.

PMID:
19519455
14.

Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm.

Gáspári Z, Vlahovicek K, Pongor S.

Bioinformatics. 2005 Aug 1;21(15):3322-3. Epub 2005 May 24.

PMID:
15914542
15.

Improving the accuracy of protein secondary structure prediction using structural alignment.

Montgomerie S, Sundararaj S, Gallin WJ, Wishart DS.

BMC Bioinformatics. 2006 Jun 14;7:301.

16.

DescFold: a web server for protein fold recognition.

Yan RX, Si JN, Wang C, Zhang Z.

BMC Bioinformatics. 2009 Dec 14;10:416. doi: 10.1186/1471-2105-10-416.

17.

Effect of using suboptimal alignments in template-based protein structure prediction.

Chen H, Kihara D.

Proteins. 2011 Jan;79(1):315-34. doi: 10.1002/prot.22885.

18.

Arby: automatic protein structure prediction using profile-profile alignment and confidence measures.

von Ohsen N, Sommer I, Zimmer R, Lengauer T.

Bioinformatics. 2004 Sep 22;20(14):2228-35. Epub 2004 Apr 1.

PMID:
15059818
19.

A comprehensive assessment of sequence-based and template-based methods for protein contact prediction.

Wu S, Zhang Y.

Bioinformatics. 2008 Apr 1;24(7):924-31. doi: 10.1093/bioinformatics/btn069. Epub 2008 Feb 22.

20.

Protein structure prediction based on sequence similarity.

Jaroszewski L.

Methods Mol Biol. 2009;569:129-56. doi: 10.1007/978-1-59745-524-4_7.

PMID:
19623489

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