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IBM Journal of Research and Development
Applications of Massively Parallel Systems   Volume 52, Number 1/2, 2008
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Advances in Rosetta protein structure prediction on massively parallel systems - References

 by S. Raman,
B. Qian,
D. Baker,
and R. C. Walker
References

  1. C. B. Anfinsen, E. Haber, M. Sela, and F. H. White, Jr., “The Kinetics of Formation of Native Ribonuclease During Oxidation of the Reduced Polypeptide Chain,” Proc. Natl. Acad. Sci. USA 47, No. 9, 1309–1314 (1961).
  2. D. Baker and A. Sali, “Protein Structure Prediction and Structural Genomics,” Science 294, No. 5540, 93–96 (2001).
  3. C. Levinthal, “Are There Pathways for Protein Folding?”, J. Chim. Phys. Pys.-Chim. Bio. 65, No. 1, 44–68 (1968).
  4. K. T. Simons, C. Kooperberg, E. Huang, and D. Baker, “Assembly of Protein Tertiary Structures from Fragments with Similar Local Sequences Using Simulated Annealing and Bayesian Scoring Functions,” J. Mol. Biol. 268, No. 1, 209–225 (1997).
  5. R. L. Dunbrack, Jr. and F. E. Cohen, “Bayesian Statistical Analysis of Protein Side-Chain Rotamer Preferences,” Protein Sci. 6, No. 8, 1661–1681 (1997).
  6. B. Kuhlman and D. Baker, “Native Protein Sequences Are Close to Optimal for Their Structures,” Proc. Natl. Acad. Sci. USA 97, No. 19, 10383–10388 (2000).
  7. K. M. Misura and D. Baker, “Progress and Challenges in High-Resolution Refinement of Protein Structure Models,” Proteins 59, No. 1, 15–29 (2005).
  8. P. Bradley, K. M. Misura, and D. Baker, “Toward High-Resolution De Novo Structure Prediction for Small Proteins,” Science 309, No. 5742, 1868–1871 (2005).
  9. Z. Li and H. A. Scheraga, “Monte-Carlo Minimization Approach to the Multiple Minima Problem in Protein Folding,” Proc. Natl. Acad. Sci. USA 84, No. 19, 6611–6615 (1987).
  10. T. Lazaridis and M. Karplus, “Effective Energy Function for Proteins in Solution,” Proteins 35, No. 2, 133–152 (1999).
  11. A. V. Morozov, T. Kortemme, K. Tsemekhman, and D. Baker, “Close Agreement Between the Orientation Dependence of Hydrogen Bonds Observed in Protein Structures and Quantum Mechanical Calculations,” Proc. Natl. Acad. Sci. USA 101, No. 18, 6946–6951 (2004).
  12. T. Kortemme, A. V. Morozov, and D. Baker, “An Orientation-Dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein–Protein Complexes,” J. Mol. Biol. 326, No. 4, 1239–1259 (2003).
  13. A. A. Canutescu and R. L. Dunbrack, Jr., “Cyclic Coordinate Descent: A Robotics Algorithm for Protein Loop Closure,” Protein Sci. 12, No. 5, 963–972 (2003).
  14. B. Kuhlman, G. Dantas, G. C. Ireton, G. Varani, B. L. Stoddard, and D. Baker, “Design of a Novel Globular Protein Fold with Atomic-Level Accuracy,” Science 302, No. 5649, 1364–1368 (2003).
  15. C. A. Rohl, C. E. Strauss, K. M. Misura, and D. Baker, “Protein Structure Prediction Using Rosetta,” Methods Enzymol. 383, No. 1, 66–93 (2004).
  16. Protein Structure Prediction Center, Genome Center, University of California, Davis; see http://predictioncenter.org/.
  17. J. Moult, K. Fidelis, A. Zemla, and T. Hubbard, “Critical Assessment of Methods of Protein Structure Prediction (CASP)-Round V,” Proteins Str. Func. Gen. 53, No. 6, 334–339 (2003).
  18. M. Snir, S. W. Otto, S. Huss-Lederman, D. W. Walker, and J. Dongarra, MPI: The Complete Reference, Cambridge, Massachusetts, London, England: The MIT Press, Cambridge, MA, London, England, 1996.
  19. R. Das, B. Qian, S. Raman, R. Vernon, J. Thompson, P. Bradley, S. Khare, et al., “Structure Prediction for CASP7 Targets Using Extensive All-Atom Refinement with Rosetta@home,” Proteins Structure Function Bioinformatics 69, No. S8, 118–128 (2007)..
  20. I. A. Wilson, for the Joint Center for Structural Genomics, Structure 2HQ7, 2007; see http://www.pdb.org/pdb/explore/explore.do?structureId=2HQ7.
  21. “Research Collaboratory for Structural Bioinformatics (RCSB)”, (sequence data); see ftp://ftp.rcsb.org/pub/pdb/derived_data/pdb_seqres.txt.


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