How to Cite

Please cite the following two papers if you use PRISM Web server.
  • Baspinar A, Cukuroglu E, Nussinov R, Keskin O, Gursoy A. PRISM: A web server and repository for prediction of protein-protein interactions and modeling their 3D complexes. Nucl. Acids Res. (2014) doi: 10.1093/nar/gku397 PubMed PMID: 24829450
  • Tuncbag N, Gursoy A, Nussinov R, Keskin O. Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat Protoc. 2011 Aug 11;6(9):1341-54. doi: 10.1038/nprot.2011.367. PubMed PMID: 21886100.

Algorithm

  • Tuncbag N, Gursoy A, Nussinov R, Keskin O. Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat Protoc. 2011 Aug 11;6(9):1341-54. doi: 10.1038/nprot.2011.367. PubMed PMID: 21886100.
  • Aytuna AS, Gursoy A, Keskin O. Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics. 2005 Jun 15;21(12):2850-5. Epub 2005 Apr 26. PubMed PMID: 15855251.

Template Set

  • Cukuroglu E, Gursoy A, Nussinov R, Keskin O (2014) Non-Redundant Unique Interface Structures as Templates for Modeling Protein Interactions. PLoS ONE 9(1): e86738. doi: 10.1371 / journal.pone.0086738. PubMed PMID: 24475173.

Evaluation

  • Tuncbag N, Keskin O, Nussinov R, Gursoy A. Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement. Proteins. 2012 Apr;80(4):1239-49. doi: 10.1002/prot.24022. Epub 2012 Jan 31. PubMed PMID: 22275112.
  • Kuzu G, Gursoy A, Nussinov R, Keskin O. Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale. J Proteome Res. 2013 Jun 7;12(6):2641-53. doi: 10.1021/pr400006k. Epub 2013 Apr 30. PubMed PMID: 23590674.

Applications

  • Guven Maiorov E, Keskin O, Gursoy A, Nussinov R. The structural network of inflammation and cancer: merits and challenges. Semin Cancer Biol. 2013 Aug;23(4):243-51. doi: 10.1016/j.semcancer.2013.05.003. Epub 2013 May 24. PubMed PMID: 23712403.
  • Engin HB, Guney E, Keskin O, Oliva B, Gursoy A. Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer. PLoS One. 2013 Nov 22;8(11):e81035. doi: 10.1371/journal.pone.0081035. PubMed PMID: 24278371.
  • Kar G, Keskin O, Fraternali F, Gursoy A. Emerging role of the ubiquitin-proteasome system as drug targets. Curr Pharm Des. 2013;19(18):3175-89. Review. PubMed PMID: 23151131.
  • Kuzu G, Keskin O, Gursoy A, Nussinov R. Constructing structural networks of signaling pathways on the proteome scale. Curr Opin Struct Biol. 2012 Jun;22(3):367-77. doi: 10.1016/j.sbi.2012.04.004. Epub 2012 May 9. Review. PubMed PMID: 22575757.
  • Kar G, Kuzu G, Keskin O, Gursoy A. Protein-protein interfaces integrated into interaction networks: implications on drug design. Curr Pharm Des. 2012;18(30):4697-705. Review. PubMed PMID: 22650259.
  • Engin HB, Gursoy A, Nussinov R, Keskin O. Network-Based Strategies Can Help Mono- and Poly-pharmacology Drug Discovery: A Systems Biology View. Curr Pharm Des. 2013 May 22. [Epub ahead of print] PubMed PMID: 23713773.
  • Acuner Ozbabacan SE, Keskin O, Nussinov R, Gursoy A. Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes. J Struct Biol. 2012 Sep;179(3):338-46. doi: 10.1016/j.jsb.2012.02.002. Epub 2012 Feb 14. PubMed PMID: 22349545.
  • Kar G, Keskin O, Nussinov R, Gursoy A. Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs. J Proteome Res. 2012 Feb 3;11(2):1196-207. doi: 10.1021/pr2009143. Epub 2012 Jan 10. PubMed PMID: 22149024.
  • Kar G, Gursoy A, Keskin O. Human cancer protein-protein interaction network: a structural perspective. PLoS Comput Biol. 2009 Dec;5(12):e1000601. doi: 10.1371/journal.pcbi.1000601. Epub 2009 Dec 11. PubMed PMID: 20011507.
  • Tuncbag N, Kar G, Gursoy A, Keskin O, Nussinov R. Towards inferring time dimensionality in protein-protein interaction networks by integrating structures: the p53 example. Mol Biosyst. 2009 Dec;5(12):1770-8. doi: 10.1039/B905661K. PubMed PMID: 19585003.

External Tools

  • Hubbard, S.J., Campbell, S.F. and Thornton, J.M. (1991) Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors. J Mol Biol, 220, 507-530. PubMed PMID: 1856871.
  • Shatsky, M., Nussinov, R. and Wolfson, H.J. (2004) A method for simultaneous alignment of multiple protein structures. Proteins, 56, 143-156. PubMed PMID: 15162494.
  • Mashiach, E., Nussinov, R. and Wolfson, H.J. (2010) FiberDock: Flexible induced-fit backbone refinement in molecular docking. Proteins, 78, 1503-1519. PubMed PMID: 20077569.

Note: Fiberdock energy scoring will be replaced by Rosetta scoring soon!
PRISM: Protein Interactions By Structural Matching
For any problems or comments please send e-mail to prism-support_group@ku.edu.tr.