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Items: 25

1.

A Structural Perspective on the Modulation of Protein-Protein Interactions with Small Molecules.

Demirel HC, Dogan T, Tuncbag N.

Curr Top Med Chem. 2018;18(8):700-713. doi: 10.2174/1568026618666180601080824. Review.

PMID:
29852872
2.

Phylogenetic and Other Conservation-Based Approaches to Predict Protein Functional Sites.

Atas H, Tuncbag N, Doğan T.

Methods Mol Biol. 2018;1762:51-69. doi: 10.1007/978-1-4939-7756-7_4.

PMID:
29594767
3.

Comparative phosphoproteomic analysis reveals signaling networks regulating monopolar and bipolar cytokinesis.

Karayel Ö, Şanal E, Giese SH, Üretmen Kagıalı ZC, Polat AN, Hu CK, Renard BY, Tuncbag N, Özlü N.

Sci Rep. 2018 Feb 2;8(1):2269. doi: 10.1038/s41598-018-20231-5.

4.

Functional Constraints on Replacing an Essential Gene with Its Ancient and Modern Homologs.

Kacar B, Garmendia E, Tuncbag N, Andersson DI, Hughes D.

MBio. 2017 Aug 29;8(4). pii: e01276-17. doi: 10.1128/mBio.01276-17.

5.

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
6.

Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways.

Khurana V, Peng J, Chung CY, Auluck PK, Fanning S, Tardiff DF, Bartels T, Koeva M, Eichhorn SW, Benyamini H, Lou Y, Nutter-Upham A, Baru V, Freyzon Y, Tuncbag N, Costanzo M, San Luis BJ, Schöndorf DC, Barrasa MI, Ehsani S, Sanjana N, Zhong Q, Gasser T, Bartel DP, Vidal M, Deleidi M, Boone C, Fraenkel E, Berger B, Lindquist S.

Cell Syst. 2017 Feb 22;4(2):157-170.e14. doi: 10.1016/j.cels.2016.12.011. Epub 2017 Jan 25.

7.

Network Modeling Identifies Patient-specific Pathways in Glioblastoma.

Tuncbag N, Milani P, Pokorny JL, Johnson H, Sio TT, Dalin S, Iyekegbe DO, White FM, Sarkaria JN, Fraenkel E.

Sci Rep. 2016 Jun 29;6:28668. doi: 10.1038/srep28668.

8.

The potential impact of recent developments in three-dimensional quantitative interaction proteomics on structural biology.

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

Expert Rev Proteomics. 2016 May;13(5):447-9. doi: 10.1080/14789450.2016.1182023. No abstract available.

9.

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package.

Tuncbag N, Gosline SJ, Kedaigle A, Soltis AR, Gitter A, Fraenkel E.

PLoS Comput Biol. 2016 Apr 20;12(4):e1004879. doi: 10.1371/journal.pcbi.1004879. eCollection 2016 Apr.

10.

Predicting Protein-Protein Interactions from the Molecular to the Proteome Level.

Keskin O, Tuncbag N, Gursoy A.

Chem Rev. 2016 Apr 27;116(8):4884-909. doi: 10.1021/acs.chemrev.5b00683. Epub 2016 Apr 13. Review.

PMID:
27074302
11.

Reconstruction of the temporal signaling network in Salmonella-infected human cells.

Budak G, Eren Ozsoy O, Aydin Son Y, Can T, Tuncbag N.

Front Microbiol. 2015 Jul 20;6:730. doi: 10.3389/fmicb.2015.00730. eCollection 2015.

12.

The PI3K/AKT/mTOR interactive pathway.

Ersahin T, Tuncbag N, Cetin-Atalay R.

Mol Biosyst. 2015 Jul;11(7):1946-54. doi: 10.1039/c5mb00101c.

PMID:
25924008
13.

Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem.

Tuncbag N, Braunstein A, Pagnani A, Huang SS, Chayes J, Borgs C, Zecchina R, Fraenkel E.

J Comput Biol. 2013 Feb;20(2):124-36. doi: 10.1089/cmb.2012.0092.

14.

SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways.

Tuncbag N, McCallum S, Huang SS, Fraenkel E.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W505-9. doi: 10.1093/nar/gks445. Epub 2012 May 25.

15.

Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement.

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

Proteins. 2012 Apr;80(4):1239-49. doi: 10.1002/prot.24022. Epub 2012 Jan 31.

PMID:
22275112
16.

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM.

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

Nat Protoc. 2011 Aug 11;6(9):1341-54. doi: 10.1038/nprot.2011.367.

PMID:
21886100
17.

Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces.

Tuncbag N, Gursoy A, Keskin O.

Phys Biol. 2011 Jun;8(3):035006. doi: 10.1088/1478-3975/8/3/035006. Epub 2011 May 13. Review.

PMID:
21572173
18.

Analysis and network representation of hotspots in protein interfaces using minimum cut trees.

Tuncbag N, Salman FS, Keskin O, Gursoy A.

Proteins. 2010 Aug 1;78(10):2283-94. doi: 10.1002/prot.22741.

PMID:
20544964
19.

HotPoint: hot spot prediction server for protein interfaces.

Tuncbag N, Keskin O, Gursoy A.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W402-6. doi: 10.1093/nar/gkq323. Epub 2010 May 5.

20.

Towards inferring time dimensionality in protein-protein interaction networks by integrating structures: the p53 example.

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

Mol Biosyst. 2009 Dec;5(12):1770-8. doi: 10.1039/B905661K.

21.

Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy.

Tuncbag N, Gursoy A, Keskin O.

Bioinformatics. 2009 Jun 15;25(12):1513-20. doi: 10.1093/bioinformatics/btp240. Epub 2009 Apr 8.

PMID:
19357097
22.

A survey of available tools and web servers for analysis of protein-protein interactions and interfaces.

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

Brief Bioinform. 2009 May;10(3):217-32. doi: 10.1093/bib/bbp001. Epub 2009 Feb 24.

23.

Architectures and functional coverage of protein-protein interfaces.

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

J Mol Biol. 2008 Sep 5;381(3):785-802. doi: 10.1016/j.jmb.2008.04.071. Epub 2008 May 6.

24.

Characterization and prediction of protein interfaces to infer protein-protein interaction networks.

Keskin O, Tuncbag N, Gursoy A.

Curr Pharm Biotechnol. 2008 Apr;9(2):67-76. Review.

PMID:
18393863
25.

HotSprint: database of computational hot spots in protein interfaces.

Guney E, Tuncbag N, Keskin O, Gursoy A.

Nucleic Acids Res. 2008 Jan;36(Database issue):D662-6. Epub 2007 Oct 24.

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