Towards inferring time dimensionality in protein–protein interaction networks by integrating structures: the p53 example† †This article is part of a Molecular BioSystems themed issue on Computational and Systems Biology.
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Ozlem Keskin | Ruth Nussinov | Nurcan Tuncbag | Gozde Kar | Attila Gursoy | R. Nussinov | O. Keskin | A. Gursoy | Nurcan Tuncbag | Gozde Kar
[1] R. Russell,et al. Protein complexes: structure prediction challenges for the 21st century. , 2005, Current opinion in structural biology.
[2] Ruth Nussinov,et al. A method for simultaneous alignment of multiple protein structures , 2004, Proteins.
[3] Wen Tang,et al. c-Abl tyrosine kinase activates p21 transcription via interaction with p53. , 2007, Journal of biochemistry.
[4] Paul W Brandt-Rauf,et al. NMR solution structure of a peptide from the mdm-2 binding domain of the p53 protein that is selectively cytotoxic to cancer cells. , 2004, Biochemistry.
[5] A. Levine,et al. Structure of the MDM2 Oncoprotein Bound to the p53 Tumor Suppressor Transactivation Domain , 1996, Science.
[6] Ozlem Keskin,et al. Architectures and functional coverage of protein-protein interfaces. , 2008, Journal of molecular biology.
[7] Jan Vijg,et al. Ku 80 Deletion Suppresses Spontaneous Tumors and Induces a p 53-Mediated DNA Damage Response , 2008 .
[8] Hongbo Zhu,et al. NOXclass: prediction of protein-protein interaction types , 2006, BMC Bioinformatics.
[9] Jan Vijg,et al. Ku80 deletion suppresses spontaneous tumors and induces a p53-mediated DNA damage response. , 2008, Cancer research.
[10] Ruth Nussinov,et al. BioInfo3D: a suite of tools for structural bioinformatics , 2004, Nucleic Acids Res..
[11] R Nussinov,et al. Towards drugs targeting multiple proteins in a systems biology approach. , 2007, Current topics in medicinal chemistry.
[12] M. Dai,et al. MDM2 Inhibits PCAF (p300/CREB-binding Protein-associated Factor)-mediated p53 Acetylation* , 2002, The Journal of Biological Chemistry.
[13] Sophia Tsoka,et al. Robustness of the p53 network and biological hackers , 2005, FEBS letters.
[14] P. Andrew Karplus,et al. Flt3 ligand structure and unexpected commonalities of helical bundles and cystine knots , 2000, Nature Structural Biology.
[15] Lan V. Zhang,et al. Evidence for dynamically organized modularity in the yeast protein–protein interaction network , 2004, Nature.
[16] N. Glansdorff,et al. Structure of the arginine repressor from Bacillus stearothermophilus , 1999, Nature Structural Biology.
[17] Ozlem Keskin,et al. PRISM: protein-protein interaction prediction by structural matching. , 2008, Methods in molecular biology.
[18] K. Komurov,et al. Revealing static and dynamic modular architecture of the eukaryotic protein interaction network , 2007, Molecular Systems Biology.
[19] Gary D Bader,et al. BIND--The Biomolecular Interaction Network Database. , 2001, Nucleic acids research.
[20] R. Carroll,et al. Mapping of phosphomonoester and apparent phosphodiester bonds of the oncogene product p53 from simian virus 40-transformed 3T3 cells. , 1986, Proceedings of the National Academy of Sciences of the United States of America.
[21] K. Kohn. Molecular interaction map of the mammalian cell cycle control and DNA repair systems. , 1999, Molecular biology of the cell.
[22] O. Keskina,et al. Towards Drugs Targeting Multiple Proteins in a Systems Biology Approach , 2008 .
[23] Gideon Schreiber,et al. Rational design of faster associating and tighter binding protein complexes , 2000, Nature Structural Biology.
[24] Gabriele Ausiello,et al. MINT: the Molecular INTeraction database , 2006, Nucleic Acids Res..
[25] Geoffrey J. Barton,et al. PIPs: human protein–protein interaction prediction database , 2008, Nucleic Acids Res..
[26] P. Bork,et al. Dynamic Complex Formation During the Yeast Cell Cycle , 2005, Science.
[27] Ozlem Keskin,et al. Similar binding sites and different partners: implications to shared proteins in cellular pathways. , 2007, Structure.
[28] Maria Victoria Schneider,et al. MINT: a Molecular INTeraction database. , 2002, FEBS letters.
[29] Ruth Nussinov,et al. MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions , 2008, Nucleic Acids Res..
[30] W Eckhart,et al. Phosphorylation sites in the amino-terminal region of mouse p53. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[31] Ozlem Keskin,et al. HotSprint: database of computational hot spots in protein interfaces , 2007, Nucleic Acids Res..
[32] Sudhir Agrawal,et al. Stabilization of E2F1 protein by MDM2 through the E2F1 ubiquitination pathway , 2005, Oncogene.
[33] Christina Kiel,et al. Analyzing protein interaction networks using structural information. , 2008, Annual review of biochemistry.
[34] Y. Zhang,et al. IntAct—open source resource for molecular interaction data , 2006, Nucleic Acids Res..
[35] R. Russell,et al. Structural systems biology: modelling protein interactions , 2006, Nature Reviews Molecular Cell Biology.
[36] J. Walker,et al. Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair , 2001, Nature.
[37] Tony Kouzarides,et al. Stimulation of E2F1/DP1 transcriptional activity by MDM2 oncoprotein , 1995, Nature.
[38] Ken Garber,et al. Missing the target: ubiquitin ligase drugs stall. , 2005, Journal of the National Cancer Institute.
[39] Philip M. Kim,et al. Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights , 2006, Science.
[40] D. Meek,et al. Phosphorylation of p53 in normal and simian virus 40-transformed NIH 3T3 cells , 1988, Molecular and cellular biology.
[41] Patrick Aloy,et al. Interrogating protein interaction networks through structural biology , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[42] Manabu Koike,et al. Ku80 can translocate to the nucleus independent of the translocation of Ku70 using its own nuclear localization signal , 1999, Oncogene.
[43] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[44] Michael Berger,et al. Tyrosine phosphorylation of Mdm2 by c‐Abl: implications for p53 regulation , 2002, The EMBO journal.
[45] J. Piette,et al. MDM2: life without p53. , 2001, Trends in genetics : TIG.
[46] Ozlem Keskin,et al. PRISM: protein interactions by structural matching , 2005, Nucleic Acids Res..
[47] W. Sellers,et al. Interaction between the retinoblastoma protein and the oncoprotein MDM2 , 1995, Nature.
[48] Ozlem Keskin,et al. Characterization and prediction of protein interfaces to infer protein-protein interaction networks. , 2008, Current pharmaceutical biotechnology.
[49] Patrick Aloy,et al. The third dimension for protein interactions and complexes. , 2002, Trends in biochemical sciences.
[50] Adam J. Smith,et al. The Database of Interacting Proteins: 2004 update , 2004, Nucleic Acids Res..
[51] Peer Bork,et al. Towards Cellular Systems in 4D , 2005, Cell.
[52] Michael Schroeder,et al. Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data , 2007, ISMB/ECCB.
[53] Andrzej Kloczkowski,et al. Functional clustering of yeast proteins from the protein-protein interaction network , 2006, BMC Bioinformatics.
[54] H. Wolfson,et al. A new, structurally nonredundant, diverse data set of protein–protein interfaces and its implications , 2004, Protein science : a publication of the Protein Society.
[55] Ozlem Keskin,et al. Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces , 2005, Bioinform..
[56] Jeong Ho Chang,et al. Structural basis for the recognition of the E2F transactivation domain by the retinoblastoma tumor suppressor. , 2002, Genes & development.
[57] Ozlem Keskin,et al. Topological properties of protein interaction networks from a structural perspective. , 2008, Biochemical Society transactions.
[58] Joost Schymkowitz,et al. Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations. , 2005, Journal of molecular biology.
[59] D. Baker,et al. Computational redesign of protein-protein interaction specificity , 2004, Nature Structural &Molecular Biology.