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Items: 1 to 20 of 90

1.

Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods.

Ohue M, Matsuzaki Y, Shimoda T, Ishida T, Akiyama Y.

BMC Proc. 2013 Dec 20;7(Suppl 7):S6. doi: 10.1186/1753-6561-7-S7-S6. Epub 2013 Dec 20.

2.

MEGADOCK: an all-to-all protein-protein interaction prediction system using tertiary structure data.

Ohue M, Matsuzaki Y, Uchikoga N, Ishida T, Akiyama Y.

Protein Pept Lett. 2014;21(8):766-78.

3.

Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions.

Zhou H, Gao S, Nguyen NN, Fan M, Jin J, Liu B, Zhao L, Xiong G, Tan M, Li S, Wong L.

Biol Direct. 2014 Apr 8;9:5. doi: 10.1186/1745-6150-9-5.

4.

MEGADOCK 3.0: a high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments.

Matsuzaki Y, Uchikoga N, Ohue M, Shimoda T, Sato T, Ishida T, Akiyama Y.

Source Code Biol Med. 2013 Sep 3;8(1):18. doi: 10.1186/1751-0473-8-18.

5.
6.

Reconstructing genome-wide protein-protein interaction networks using multiple strategies with homologous mapping.

Lo YS, Huang SH, Luo YC, Lin CY, Yang JM.

PLoS One. 2015 Jan 20;10(1):e0116347. doi: 10.1371/journal.pone.0116347. eCollection 2015.

7.

Stringent DDI-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions.

Zhou H, Rezaei J, Hugo W, Gao S, Jin J, Fan M, Yong CH, Wozniak M, Wong L.

BMC Syst Biol. 2013;7 Suppl 6:S6. doi: 10.1186/1752-0509-7-S6-S6. Epub 2013 Dec 13.

8.

Evaluating template-based and template-free protein-protein complex structure prediction.

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

Brief Bioinform. 2014 Mar;15(2):169-76. doi: 10.1093/bib/bbt047. Epub 2013 Jul 1.

9.

Evolutionary analysis and interaction prediction for protein-protein interaction network in geometric space.

Huang L, Liao L, Wu CH.

PLoS One. 2017 Sep 8;12(9):e0183495. doi: 10.1371/journal.pone.0183495. eCollection 2017.

10.

Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information.

Tuncbag N, Keskin O, Nussinov R, Gursoy A.

Methods Mol Biol. 2017;1558:255-270. doi: 10.1007/978-1-4939-6783-4_12.

PMID:
28150242
11.

Network analysis and in silico prediction of protein-protein interactions with applications in drug discovery.

Murakami Y, Tripathi LP, Prathipati P, Mizuguchi K.

Curr Opin Struct Biol. 2017 Jun;44:134-142. doi: 10.1016/j.sbi.2017.02.005. Epub 2017 Mar 30. Review.

PMID:
28364585
12.

Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators.

Murakami Y, Mizuguchi K.

BMC Bioinformatics. 2014 Jun 23;15:213. doi: 10.1186/1471-2105-15-213.

13.

Predicting genome-scale Arabidopsis-Pseudomonas syringae interactome using domain and interolog-based approaches.

Sahu SS, Weirick T, Kaundal R.

BMC Bioinformatics. 2014;15 Suppl 11:S13. doi: 10.1186/1471-2105-15-S11-S13. Epub 2014 Oct 21.

14.

Prediction and characterization of protein-protein interaction networks in swine.

Wang F, Liu M, Song B, Li D, Pei H, Guo Y, Huang J, Zhang D.

Proteome Sci. 2012 Jan 10;10(1):2. doi: 10.1186/1477-5956-10-2.

15.

Uncovering New Pathogen-Host Protein-Protein Interactions by Pairwise Structure Similarity.

Cui T, Li W, Liu L, Huang Q, He ZG.

PLoS One. 2016 Jan 22;11(1):e0147612. doi: 10.1371/journal.pone.0147612. eCollection 2016.

16.

Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis.

You ZH, Lei YK, Zhu L, Xia J, Wang B.

BMC Bioinformatics. 2013;14 Suppl 8:S10. doi: 10.1186/1471-2105-14-S8-S10. Epub 2013 May 9.

17.

In silico structure-based approaches to discover protein-protein interaction-targeting drugs.

Shin WH, Christoffer CW, Kihara D.

Methods. 2017 Aug 9. pii: S1046-2023(17)30208-6. doi: 10.1016/j.ymeth.2017.08.006. [Epub ahead of print] Review.

PMID:
28802714
18.

Computational probing protein-protein interactions targeting small molecules.

Wang YC, Chen SL, Deng NY, Wang Y.

Bioinformatics. 2016 Jan 15;32(2):226-34. doi: 10.1093/bioinformatics/btv528. Epub 2015 Sep 28.

PMID:
26415726
19.

Comparative analysis and assessment of M. tuberculosis H37Rv protein-protein interaction datasets.

Zhou H, Wong L.

BMC Genomics. 2011 Nov 30;12 Suppl 3:S20. doi: 10.1186/1471-2164-12-S3-S20. Epub 2011 Nov 30.

20.

In silico screening of protein-protein interactions with all-to-all rigid docking and clustering: an application to pathway analysis.

Matsuzaki Y, Matsuzaki Y, Sato T, Akiyama Y.

J Bioinform Comput Biol. 2009 Dec;7(6):991-1012.

PMID:
20014475

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