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Ensemble-Based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants

Demir, Özlem, Baronio, Roberta, Salehi, Faezeh, Wassman, Christopher D., Hall, Linda, Hatfield, G. Wesley, Chamberlin, Richard, Kaiser, Peter, Lathrop, Richard H., Amaro, Rommie E.·2011·PLoS Computational Biology

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Research works printed but not linked: 39

  1. AJ Levine, 2006, The P53 pathway: what questions remain to be explored?, Cell Death Differ, 13, 1027, 10.1038/sj.cdd.4401910 · DOI · Paper page
  2. B Vogelstein, 2000, Surfing the p53 network., Nature, 408, 307, 10.1038/35042675 · DOI · Paper page
  3. KH Vousden, 2002, Live or let die: the cell's response to p53., Nat Rev Cancer, 2, 594, 10.1038/nrc864 · DOI · Paper page
  4. AC Joerger, 2010, The tumor suppressor p53: from structures to drug discovery., Cold Spring Harb Perspect Biol, 2, a000919, 10.1101/cshperspect.a000919 · DOI · Paper page
  5. DM Feldser, 2010, Stage-specific sensitivity to p53 restoration during lung cancer progression., Nature, 468, 572, 10.1038/nature09535 · DOI · Paper page
  6. MR Junttila, 2010, Selective activation of p53-mediated tumour suppression in high-grade tumours., Nature, 468, 567, 10.1038/nature09526 · DOI · Paper page
  7. VJ Bykov, 2002, Mutant p53-dependent growth suppression distinguishes PRIMA-1 from known anticancer drugs: a statistical analysis of information in the National Cancer Institute database., Carcinogenesis, 23, 2011, 10.1093/carcin/23.12.2011 · DOI · Paper page
  8. VJ Bykov, 2005, Reactivation of mutant p53 and induction of apoptosis in human tumor cells by maleimide analogs., J Biol Chem, 280, 30384, 10.1074/jbc.M501664200 · DOI · Paper page
  9. BA Foster, 1999, Pharmacological rescue of mutant p53 conformation and function., Science, 286, 2507, 10.1126/science.286.5449.2507 · DOI · Paper page
  10. S North, 2002, Restoration of wild-type conformation and activity of a temperature-sensitive mutant of p53 (p53(V272M)) by the cytoprotective aminothiol WR1065 in the esophageal cancer cell line TE-1., Mol Carcinog, 33, 181, 10.1002/mc.10038 · DOI
  11. AM Wieczorek, 1996, Structure-based rescue of common tumor-derived p53 mutants., Nat Med, 2, 1143, 10.1038/nm1096-1143 · DOI
  12. RK Brachmann, 1998, Genetic selection of intragenic suppressor mutations that reverse the effect of common p53 cancer mutations., EMBO J, 17, 1847, 10.1093/emboj/17.7.1847 · DOI · Paper page
  13. TE Baroni, 2004, A global suppressor motif for p53 cancer mutants., Proc Natl Acad Sci U S A, 101, 4930, 10.1073/pnas.0401162101 · DOI
  14. R Baronio, 2010, All-codon scanning identifies p53 cancer rescue mutations., Nucleic Acids Res, 38, 7079, 10.1093/nar/gkq571 · DOI
  15. AC Joerger, 2004, Crystal structure of a superstable mutant of human p53 core domain. Insights into the mechanism of rescuing oncogenic mutations., J Biol Chem, 279, 1291, 10.1074/jbc.M309732200 · DOI · Paper page
  16. AC Joerger, 2006, Structural basis for understanding oncogenic p53 mutations and designing rescue drugs., Proc Natl Acad Sci U S A, 103, 15056, 10.1073/pnas.0607286103 · DOI · Paper page
  17. AC Joerger, 2005, Structures of p53 cancer mutants and mechanism of rescue by second-site suppressor mutations., J Biol Chem, 280, 16030, 10.1074/jbc.M500179200 · DOI · Paper page
  18. HC Ang, 2006, Effects of common cancer mutations on stability and DNA binding of full-length p53 compared with isolated core domains., J Biol Chem, 281, 21934, 10.1074/jbc.M604209200 · DOI · Paper page
  19. AN Bullock, 2000, Quantitative analysis of residual folding and DNA binding in mutant p53 core domain: definition of mutant states for rescue in cancer therapy., Oncogene, 19, 1245, 10.1038/sj.onc.1203434 · DOI · Paper page
  20. VB Chen, 2010, MolProbity: all-atom structure validation for macromolecular crystallography., Acta Crystallogr D Biol Crystallogr, 66, 12, 10.1107/S0907444909042073 · DOI · Paper page
  21. R Rodriguez, 1998, Homology modeling, model and software evaluation: three related resources., Bioinformatics, 14, 523, 10.1093/bioinformatics/14.6.523 · DOI · Paper page
  22. WL Jorgensen, 1983, Comparison of Simple Potential Functions for Simulating Liquid Water., J Chem Phys, 79, 926, 10.1063/1.445869 · DOI · Paper page
  23. V Hornak, 2006, Comparison of multiple amber force fields and development of improved protein backbone parameters., Proteins Struct Funct Bioinf, 65, 712, 10.1002/prot.21123 · DOI · Paper page
  24. GJ Martyna, 1994, Constant-Pressure Molecular-Dynamics Algorithms., J Chem Phys, 101, 4177, 10.1063/1.467468 · DOI · Paper page
  25. SE Feller, 1995, Constant-Pressure Molecular-Dynamics Simulation - the Langevin Piston Method., J Chem Phys, 103, 4613, 10.1063/1.470648 · DOI · Paper page
  26. T Darden, 1999, New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations., Structure, 7, R55, 10.1016/S0969-2126(99)80033-1 · DOI · Paper page
  27. J-P Ryckaert, 1977, Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes., J Comput Phys, 23, 327, 10.1016/0021-9991(77)90098-5 · DOI · Paper page
  28. S Miyamoto, 1992, Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models., J Comput Chem, 13, 952, 10.1002/jcc.540130805 · DOI · Paper page
  29. JC Phillips, 2005, Scalable molecular dynamics with NAMD., J Comput Chem, 26, 1781, 10.1002/jcc.20289 · DOI · Paper page
  30. FM Boeckler, 2008, Targeted rescue of a destabilized mutant of p53 by an in silico screened drug., Proc Natl Acad Sci U S A, 105, 10360, 10.1073/pnas.0805326105 · DOI · Paper page
  31. PV Nikolova, 2000, Mechanism of rescue of common p53 cancer mutations by second-site suppressor mutations., EMBO J, 19, 370, 10.1093/emboj/19.3.370 · DOI · Paper page
  32. PV Nikolova, 1998, Semirational design of active tumor suppressor p53 DNA binding domain with enhanced stability., Proc Natl Acad Sci U S A, 95, 14675, 10.1073/pnas.95.25.14675 · DOI · Paper page
  33. X Daura, 1999, Peptide folding: When simulation meets experiment., Angew Chem-Int Edit, 38, 236, 10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M · DOI · Paper page
  34. B Hess, 2008, GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation., J Chem Theory Comput, 4, 435, 10.1021/ct700301q · DOI · Paper page
  35. RS Sikorski, 1989, A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae., Genetics, 122, 19, 10.1093/genetics/122.1.19 · DOI · Paper page
  36. J Hill, 1991, DMSO-enhanced whole cell yeast transformation., Nucleic Acids Res, 19, 5791, 10.1093/nar/19.20.5791 · DOI · Paper page
  37. SA Danziger, 2009, Predicting Positive p53 Cancer Rescue Regions Using Most Informative Positive (MIP) Active Learning., PLOS Comput Biol, 5, e1000498, 10.1371/journal.pcbi.1000498 · DOI
  38. SMA Rauf, 2009, A graph theoretical approach to the effect of mutation on the flexibility of the DNA binding domain of p53 protein., Chem Papers, 63, 654
  39. AN Bullock, 1997, Thermodynamic stability of wild-type and mutant p53 core domain., Proc Natl Acad Sci U S A, 94, 14338, 10.1073/pnas.94.26.14338 · DOI · Paper page

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Metadata

Authors
Demir, Ö., Baronio, R., Salehi, F., Wassman, C. D., Hall, L., Hatfield, G. W., Chamberlin, R., Kaiser, P., Lathrop, R. H., & Amaro, R. E.
Venue
PLoS Computational Biology
Published
2011-10-20
Volume
7
Issue
10
Pages
e1002238
ISSN
1553-7358
Cited by
39
References
6
Language
en

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CoChat. (2026). Citation check: Ensemble-Based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants. https://app.cochat.ai/papers/10.1371/journal.pcbi.1002238
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Demir, Ö., Baronio, R., Salehi, F., Wassman, C. D., Hall, L., Hatfield, G. W., Chamberlin, R., Kaiser, P., Lathrop, R. H., & Amaro, R. E. (2011). Ensemble-Based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants. PLoS Computational Biology. https://doi.org/10.1371/journal.pcbi.1002238

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