IBM®
Skip to main content
    Country/region [change]    Terms of use
 
 
 
    Home    Products    Services & solutions    Support & downloads    My account    

IBM Journal of Research and Development

Applications of Massively Parallel Systems   Volume 52, Number 1/2, 2008
Table of contents: HTMLPDF This article: HTMLPDF   Copyright info

EUDOC on the IBM Blue Gene/L system: Accelerating the transfer of drug discoveries from laboratory to patient - References

by Y.-P. Pang,
T. J. Mullins,
B. A. Swartz,
J. S. McAllister,
B. E. Smith,
C. J. Archer,
R. G. Musselman,
A. E. Peters,
B. P. Wallenfelt,
and K. W. Pinnow
References

  1. Y.-P. Pang, “In Silico Drug Discovery: Solving the ‘Target-Rich and Lead-Poor’ Imbalance Using the Genome-to-Drug-Lead Paradigm,” Clin. Pharmacol. Ther. 81, No. 1, 30–34 (2007).
  2. Y.-P. Pang, E. Perola, K. Xu, and F. G. Prendergast, “EUDOC: A Computer Program for Identification of Drug Interaction Sites in Macromolecules and Drug Leads from Chemical Databases,” J. Comput. Chem. 22, No. 15, 1750–1771 (2001).
  3. Q. Wang and Y.-P. Pang, “Accurate Reproduction of 161 Small-Molecule Complex Crystal Structures Using the EUDOC Program: Expanding the Use of EUDOC to Supramolecular Chemistry,” PLoS ONE 2, No. 6, e531(2007).
  4. E. Perola, K. Xu, T. M. Kollmeyer, S. H. Kaufmann, F. G. Prendergast, and Y.-P. Pang, “Successful Virtual Screening of a Chemical Database for Farnesyltransferase Inhibitor Leads,” J. Med. Chem. 43, No. 401–408 (2000).
  5. M. A. Miller, “Chemical Database Techniques in Drug Discovery,” Nat. Rev. Drug Discov. 1, No. 3, 220–227 (2002).
  6. M. L. Raves, M. Harel, Y.-P. Pang, I. Silman, A. P. Kozikowski, and J. L. Sussman, “Structure of Acetylcholinesterase Complexed with the Nootropic Alkaloid, (−)-Huperzine A,” Nat. Struct. Biol. 4, No. 1, 57–63 (1997).
  7. Y.-P. Pang, K. Xu, T. M. Kollmeyer, E. Perola, W. J. McGrath, D. T. Green, and W. F. Mangel, “Discovery of a New Inhibitor Lead of Adenovirus Proteinase: Steps Toward Selective, Irreversible Inhibitors of Cysteine Proteinases,” FEBS Lett. 502, No. 3, 93–97 (2001).
  8. H. Sun, Y.-P. Pang, O. Lockridge, and S. Brimijoin, “Re-engineering Butyrylcholinesterase as a Cocaine Hydrolase,” Mol. Pharmacol. 62, No. 2, 220–224 (2002).
  9. A. J. Dooley, N. Shindo, B. Taggart, J. G. Park, and Y.-P. Pang, “From Genome to Drug Lead: Identification of a Small-Molecule Inhibitor of the SARS Virus,” Bioorg. Med. Chem. Lett. 16, No. 4, 830–833 (2006).
  10. J. G. Park, P. C. Sill, E. F. Makiyi, A. T. Garcia-Sosa, C. B. Millard, J. J. Schmidt, and Y.-P. Pang, “Serotype-Selective, Small-Molecule Inhibitors of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A,” Bioorg. Med. Chem. 14, No. 2, 395–408 (2006).
  11. J. Tang, J. G. Park, C. B. Millard, J. J. Schmidt, and Y.-P. Pang, “Computer-Aided Lead Optimization: Improved Small-Molecule Inhibitor of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A,” PLoS ONE 2, No. 8, e761(2007).
  12. J. C. Venter, M. D. Adams, E. W. Myers, P. W. Li, R. J. Mural, G. G. Sutton, H. O. Smith, et al., “The Sequence of the Human Genome,” Science 291, No. 5507, 1304–1351 (2001).
  13. R. E. Banks, M. J. Dunn, D. F. Hochstrasser, J. C. Sanchez, W. Blackstock, D. J. Pappin, and P. J. Selby, “Proteomics: New Perspectives, New Biomedical Opportunities,” Lancet 356, No. 9243, 1749–1756 (2000).
  14. Y.-P. Pang, “Novel Acetylcholinesterase Target Site for Malaria Mosquito Control,” PLoS ONE 1, No. 1, e58(2006).
  15. Y.-P. Pang, “Species Marker for Developing Novel and Safe Pesticides,” Bioorg. Med. Chem. Lett. 17, No. 197–199 (2007).
  16. S. K. Burley, S. C. Almo, J. B. Bonanno, M. Capel, M. R. Chance, T. Gaasterland, D. W. Lin, A. Sali, F. W. Studier, and S. Swaminathan, “Structural Genomics: Beyond the Human Genome Project,” Nat. Genet. 23, No. 2, 151–157 (1999).
  17. R. L. DesJarlais, G. L. Seibel, I. D. Kuntz, P. S. Furth, J. C. Alvarez, P. R. Ortiz de Montellano, D. L. DeCamp, L. M. Babe, and C. S. Craik, “Structure-Based Design of Nonpeptide Inhibitors Specific for the Human Immunodeficiency Virus 1 Protease,” Proc. Natl. Acad. Sci. USA 87, No. 17, 6644–6648 (1990).
  18. D. E. Koshland, “The Key–Lock Theory and the Induced Fit Theory,” Angew. Chem. Int. Ed. Engl. 33, No. 23–24, 2375–2378 (1995).
  19. A. S. Burgen, “Conformational Changes and Drug Action,” Fed. Proc. 40, No. 13, 2723–2728 (1981).
  20. R. F. Bruns, “Conformational Induction Versus Conformational Selection: Evidence from Allosteric Enhancers,” Trends Pharmacol. Sci. 17, No. 5, 189–191 (1996).
  21. T. Kenakin, “Receptor Conformational Induction Versus Selection: All Part of the Same Energy Landscape: Agonists Can Differentially Stabilize Multiple Active States of Receptors,” Trends Pharmacol. Sci. 17, No. 190–191 (1996).
  22. Y.-P. Pang, N. D. Silva, C. Hydock, and F. G. Prendergast, “Docking Studies on the Complexed and Uncomplexed FKBP12 Structures with Bound and Unbound Ligands: An Implication of Conformational Selection Mechanism for Binding,” J. Mol. Model. 3, No. 240–248 (1997).
  23. Q. Wang and Y.-P. Pang, “Preference of Small Molecules for Local Minimum Conformations when Binding to Proteins,” PLoS ONE 2, No. 9, e820(2007).
  24. Q. Wang and Y.-P. Pang, “Normal-Mode-Analysis-Monitored Energy Minimization Procedure for Generating Small-Molecule Bound Conformations,” PLoS ONE 2, No. 10, e1025(2007).
  25. Y.-P. Pang, “Three-Dimensional Model of a Substrate-Bound SARS Chymotrypsin-Like Cysteine Proteinase Predicted by Multiple Molecular Dynamics Simulations: Catalytic Efficiency Regulated by Substrate Binding,” Proteins 57, No. 747–757 (2004).
  26. A. Gara, M. A. Blumrich, D. Chen, G. L.-T. Chiu, P. Coteus, M. E. Giampapa, R. A. Haring, et al., “Overview of the Blue Gene/L System Architecture,” IBM J. Res. & Dev. 49, No. 2/3, 195–212 (2005).
  27. W. Pulleyblank, “How to Build a Supercomputer,” IEE Rev. 50, No. 1, 48–52 (2004).
  28. V. Salapura, R. Walkup, and A. Gara, “Exploiting Workload Parallelism for Performance and Power Optimization in Blue Gene,” Micro IEEE 26, No. 5, 67–81 (2006).
  29. J. Moreira, “Delivering Teraflops: An Account of How Blue Gene Was Brought to Life,” presented at Modern Computing, IEEE John Vincent Atanasoff 2006 International Symposium, 2006.
  30. A. A. Bright, M. R. Ellavsky, A. Gara, R. A. Haring, G. V. Kopcsay, R. F. Lembach, J. A. Marcella, M. Ohmacht, and V. Salapura, “Creating the Blue Gene/L Supercomputer from Low Power Systom-on-a-Chip ASICs,” IEEE International Solid-State Circuits Conference, Digest of Technical Papers, February 2005, pp. 188–189.
  31. F. Allen, G. Almasi, W. Andreoni, D. Beece, B. J. Berne, A. Bright, J. Brunheroto, et al., “Blue Gene: A Vision for Protein Science using a Petaflop Supercomputer,” IBM Syst. J. 40, No. 2, 310–327 (2001).
  32. J. E. Moreira, G. Almási, C. Archer, R. Bellofatto, P. Bergner, J. R. Brunheroto, M. Brutman, et al., “Blue Gene/L Programming and Operating Environment,” IBM J. Res. & Dev. 49, No. 2/3, 367–376 (2005).
  33. S. Chatterjee, L. R. Bachega, P. Bergner, K. A. Dockser, J. A. Gunnels, M. Gupta, F. G. Gustavson, et al., “Design and Exploitation of a High-Performance SIMD Floating-Point Unit for Blue Gene/L,” IBM J. Res. & Dev. 49, No. 2/3, 377–392 (2005).
  34. Y.-P. Pang, K. Xu, J. El Yazal, and F. G. Prendergast, “Successful Molecular Dynamics Simulation of the Zinc-Bound Farnesyltransferase Using the Cationic Dummy Atom Approach,” Protein Sci. 9, No. 1857–1865 (2000).
  35. B. Walkup, “Blue Gene/L System and Optimization Tips”; see http://scv.bu.edu/documentation/presentations/BGL/BG_optimization.pdf.
  36. G. Almási, C. Archer, J. G. Castaños, M. Gupta, X. Martorell, J. E. Moreira, W. Gropp, S. Rus, and B. Toonen, “MPI on BlueGene/L: Designing an Efficient General Purpose Messaging Solution for a Large Cellular System,” Proceedings of the 10th European PVM/MPI Users' Group Meeting, Venice, Italy, September 29–October 2, 2003; see https://asc.llnl.gov/computing_resources/bluegenel/pdf/mpi.pdf.
  37. C. C. Lee and D. T. Lee, “A Simple On-line Bin-Packing Algorithm,” J. ACM 32, No. 3, 562–572 (1985).
  38. A. C.-C. Yao, “New Algorithms for Bin-Packing,” J. ACM 27, No. 2, 207–227 (1980).


    About IBMPrivacyContact