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Results: 1 to 20 of 129

Similar articles for PubMed (Select 18214977)

1.

A combination of rescoring and refinement significantly improves protein docking performance.

Pierce B, Weng Z.

Proteins. 2008 Jul;72(1):270-9. doi: 10.1002/prot.21920.

2.

ZRANK: reranking protein docking predictions with an optimized energy function.

Pierce B, Weng Z.

Proteins. 2007 Jun 1;67(4):1078-86.

PMID:
17373710
3.

Integrating atom-based and residue-based scoring functions for protein-protein docking.

Vreven T, Hwang H, Weng Z.

Protein Sci. 2011 Sep;20(9):1576-86. doi: 10.1002/pro.687. Epub 2011 Aug 8.

4.

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
5.

Replica exchange improves sampling in low-resolution docking stage of RosettaDock.

Zhang Z, Lange OF.

PLoS One. 2013 Aug 29;8(8):e72096. doi: 10.1371/journal.pone.0072096. eCollection 2013.

6.

RDOCK: refinement of rigid-body protein docking predictions.

Li L, Chen R, Weng Z.

Proteins. 2003 Nov 15;53(3):693-707.

PMID:
14579360
7.

CyClus: a fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body protein-protein docking decoys.

Omori S, Kitao A.

Proteins. 2013 Jun;81(6):1005-16. doi: 10.1002/prot.24252. Epub 2013 Feb 27.

PMID:
23344972
8.

Protein-protein docking with F(2)Dock 2.0 and GB-rerank.

Chowdhury R, Rasheed M, Keidel D, Moussalem M, Olson A, Sanner M, Bajaj C.

PLoS One. 2013;8(3):e51307. doi: 10.1371/journal.pone.0051307. Epub 2013 Mar 6.

9.

How different from random are docking predictions when ranked by scoring functions?

Feliu E, Oliva B.

Proteins. 2010 Dec;78(16):3376-85. doi: 10.1002/prot.22844. Epub 2010 Sep 16.

PMID:
20848549
10.

IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking.

Su C, Nguyen TD, Zheng J, Kwoh CK.

BMC Bioinformatics. 2014;15 Suppl 16:S9. doi: 10.1186/1471-2105-15-S16-S9. Epub 2014 Dec 8.

11.
12.

Improving ranking of models for protein complexes with side chain modeling and atomic potentials.

Viswanath S, Ravikant DV, Elber R.

Proteins. 2013 Apr;81(4):592-606. doi: 10.1002/prot.24214. Epub 2012 Dec 24.

PMID:
23180599
13.

Refining near-native protein-protein docking decoys by local resampling and energy minimization.

Liang S, Wang G, Zhou Y.

Proteins. 2009 Aug 1;76(2):309-16. doi: 10.1002/prot.22343.

14.
15.

Performance of ZDOCK in CAPRI rounds 20-26.

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

Proteins. 2013 Dec;81(12):2175-82. doi: 10.1002/prot.24432.

17.

Predicting protein complex geometries with a neural network.

Chae MH, Krull F, Lorenzen S, Knapp EW.

Proteins. 2010 Mar;78(4):1026-39. doi: 10.1002/prot.22626.

PMID:
19938153
18.

The RosettaDock server for local protein-protein docking.

Lyskov S, Gray JJ.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W233-8. doi: 10.1093/nar/gkn216. Epub 2008 Apr 28.

19.

Accelerating protein docking in ZDOCK using an advanced 3D convolution library.

Pierce BG, Hourai Y, Weng Z.

PLoS One. 2011;6(9):e24657. doi: 10.1371/journal.pone.0024657. Epub 2011 Sep 19.

20.
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