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.