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Items: 1 to 20 of 108

1.

Accelerated protein structure comparison using TM-score-GPU.

Hung LH, Samudrala R.

Bioinformatics. 2012 Aug 15;28(16):2191-2. doi: 10.1093/bioinformatics/bts345. Epub 2012 Jun 19.

2.

GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition.

Hung LH, Guerquin M, Samudrala R.

BMC Res Notes. 2011 Apr 1;4:97. doi: 10.1186/1756-0500-4-97.

3.

fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data.

Hung LH, Samudrala R.

Bioinformatics. 2014 Jun 15;30(12):1774-6. doi: 10.1093/bioinformatics/btu098. Epub 2014 Feb 14.

4.

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score.

Pandit SB, Skolnick J.

BMC Bioinformatics. 2008 Dec 12;9:531. doi: 10.1186/1471-2105-9-531.

5.

I-TASSER server for protein 3D structure prediction.

Zhang Y.

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

6.

Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA.

Mrozek D, Brożek M, Małysiak-Mrozek B.

J Mol Model. 2014 Feb;20(2):2067. doi: 10.1007/s00894-014-2067-1. Epub 2014 Jan 31.

7.

ClusCo: clustering and comparison of protein models.

Jamroz M, Kolinski A.

BMC Bioinformatics. 2013 Feb 22;14:62. doi: 10.1186/1471-2105-14-62.

8.

Accelerating large-scale protein structure alignments with graphics processing units.

Pang B, Zhao N, Becchi M, Korkin D, Shyu CR.

BMC Res Notes. 2012 Feb 22;5:116. doi: 10.1186/1756-0500-5-116.

9.

CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction applications.

Lei G, Dou Y, Wan W, Xia F, Li R, Ma M, Zou D.

BMC Genomics. 2012;13 Suppl 1:S14. doi: 10.1186/1471-2164-13-S1-S14. Epub 2012 Jan 17.

10.

How significant is a protein structure similarity with TM-score = 0.5?

Xu J, Zhang Y.

Bioinformatics. 2010 Apr 1;26(7):889-95. doi: 10.1093/bioinformatics/btq066. Epub 2010 Feb 17.

11.

Quality assessment of modeled protein structure using physicochemical properties.

Rana PS, Sharma H, Bhattacharya M, Shukla A.

J Bioinform Comput Biol. 2015 Apr;13(2):1550005. doi: 10.1142/S0219720015500055. Epub 2014 Dec 19.

PMID:
25524475
12.

Sub-AQUA: real-value quality assessment of protein structure models.

Yang YD, Spratt P, Chen H, Park C, Kihara D.

Protein Eng Des Sel. 2010 Aug;23(8):617-32. doi: 10.1093/protein/gzq030. Epub 2010 Jun 4.

13.
14.

GPU-FS-kNN: a software tool for fast and scalable kNN computation using GPUs.

Arefin AS, Riveros C, Berretta R, Moscato P.

PLoS One. 2012;7(8):e44000. doi: 10.1371/journal.pone.0044000. Epub 2012 Aug 28.

15.

TM-align: a protein structure alignment algorithm based on the TM-score.

Zhang Y, Skolnick J.

Nucleic Acids Res. 2005 Apr 22;33(7):2302-9. Print 2005.

16.

Fully 3D list-mode time-of-flight PET image reconstruction on GPUs using CUDA.

Cui JY, Pratx G, Prevrhal S, Levin CS.

Med Phys. 2011 Dec;38(12):6775-86. doi: 10.1118/1.3661998.

PMID:
22149859
17.

Ab initio modeling of small proteins by iterative TASSER simulations.

Wu S, Skolnick J, Zhang Y.

BMC Biol. 2007 May 8;5:17.

18.

Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS.

Davis NA, Pandey A, McKinney BA.

Bioinformatics. 2011 Jan 15;27(2):284-5. doi: 10.1093/bioinformatics/btq638. Epub 2010 Nov 25.

19.

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests.

Mariani V, Biasini M, Barbato A, Schwede T.

Bioinformatics. 2013 Nov 1;29(21):2722-8. doi: 10.1093/bioinformatics/btt473. Epub 2013 Aug 27.

20.

GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU.

Su X, Wang X, Jing G, Ning K.

Bioinformatics. 2014 Apr 1;30(7):1031-3. doi: 10.1093/bioinformatics/btt736. Epub 2013 Dec 19.

PMID:
24363375

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