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Items: 1 to 20 of 24

1.

A multidomain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes.

Karaca E, Bonvin AM.

Structure. 2011 Apr 13;19(4):555-65. doi: 10.1016/j.str.2011.01.014.

2.

Towards the prediction of protein interaction partners using physical docking.

Wass MN, Fuentes G, Pons C, Pazos F, Valencia A.

Mol Syst Biol. 2011 Feb 15;7:469. doi: 10.1038/msb.2011.3.

3.

Three-dimensional modeling of protein interactions and complexes is going 'omics.

Stein A, Mosca R, Aloy P.

Curr Opin Struct Biol. 2011 Apr;21(2):200-8. doi: 10.1016/j.sbi.2011.01.005. Epub 2011 Feb 12. Review.

PMID:
21320770
4.

Performance of ZDOCK and ZRANK in CAPRI rounds 13-19.

Hwang H, Vreven T, Pierce BG, Hung JH, Weng Z.

Proteins. 2010 Nov 15;78(15):3104-10. doi: 10.1002/prot.22764.

5.

Protein-protein docking benchmark version 4.0.

Hwang H, Vreven T, Janin J, Weng Z.

Proteins. 2010 Nov 15;78(15):3111-4. doi: 10.1002/prot.22830.

6.

Ultra-fast FFT protein docking on graphics processors.

Ritchie DW, Venkatraman V.

Bioinformatics. 2010 Oct 1;26(19):2398-405. doi: 10.1093/bioinformatics/btq444. Epub 2010 Aug 4.

PMID:
20685958
7.

Three-dimensional structural view of the central metabolic network of Thermotoga maritima.

Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, Godzik A.

Science. 2009 Sep 18;325(5947):1544-9. doi: 10.1126/science.1174671.

8.

Pushing structural information into the yeast interactome by high-throughput protein docking experiments.

Mosca R, Pons C, Fernández-Recio J, Aloy P.

PLoS Comput Biol. 2009 Aug;5(8):e1000490. doi: 10.1371/journal.pcbi.1000490. Epub 2009 Aug 28.

9.

Protein-protein docking dealing with the unknown.

Moreira IS, Fernandes PA, Ramos MJ.

J Comput Chem. 2010 Jan 30;31(2):317-42. doi: 10.1002/jcc.21276. Review.

PMID:
19462412
10.

Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles.

Chaudhury S, Gray JJ.

J Mol Biol. 2008 Sep 12;381(4):1068-87. doi: 10.1016/j.jmb.2008.05.042. Epub 2008 May 24.

11.

Automatic prediction of protein interactions with large scale motion.

Schneidman-Duhovny D, Nussinov R, Wolfson HJ.

Proteins. 2007 Dec 1;69(4):764-73.

PMID:
17886339
12.

The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI.

Wiehe K, Pierce B, Tong WW, Hwang H, Mintseris J, Weng Z.

Proteins. 2007 Dec 1;69(4):719-25.

PMID:
17803212
13.

Implicit flexibility in protein docking: cross-docking and local refinement.

Król M, Chaleil RA, Tournier AL, Bates PA.

Proteins. 2007 Dec 1;69(4):750-7.

PMID:
17671977
14.

Integrating statistical pair potentials into protein complex prediction.

Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, Weng Z.

Proteins. 2007 Nov 15;69(3):511-20.

PMID:
17623839
15.

PIPER: an FFT-based protein docking program with pairwise potentials.

Kozakov D, Brenke R, Comeau SR, Vajda S.

Proteins. 2006 Nov 1;65(2):392-406.

PMID:
16933295
16.
17.

Docking essential dynamics eigenstructures.

Mustard D, Ritchie DW.

Proteins. 2005 Aug 1;60(2):269-74.

PMID:
15981272
18.

ZDOCK: an initial-stage protein-docking algorithm.

Chen R, Li L, Weng Z.

Proteins. 2003 Jul 1;52(1):80-7.

PMID:
12784371
19.

A novel shape complementarity scoring function for protein-protein docking.

Chen R, Weng Z.

Proteins. 2003 May 15;51(3):397-408.

PMID:
12696051
20.

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