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Applications of Massively Parallel Systems
Volume 52, Number 1/2, 2008
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Ligand discovery on massively parallel systems - References
by S. R.
Shave
,
P.
Taylor
,
M.
Walkinshaw
,
L.
Smith
,
J.
Hardy
,
and A.
Trew
References
A. L. Hopkins and C. R. Groom, “The Druggable Genome,”
Nat. Rev. Drug Discovery
1
, No. 9, 727–730 (2002).
J. Drews, “Drug Discovery: A Historical Perspective,”
Science
287
, No. 5460, 1960–1964 (2000).
W. P. Walters, M. T. Stahl, and M. A. Murcko, “Virtual Screening—An Overview,”
Drug Discovery Today
3
, No. 4, 160–178 (1998).
D. B. Kitchen, H. Decornez, J. R. Furr, and J. Bajorath, “Docking and Scoring in Virtual Screening for Drug Discovery: Methods and Applications,”
Nat. Rev. Drug Discovery
3
, No. 11, 935–949 (2004).
P. D. Lyne, “Structure-Based Virtual Screening: an Overview,”
Drug Discovery Today
7
, No. 20, 1047–1055 (2002).
C. A. Lipinski, F. Lombardo, B. W. Dominy, and P. J. Feeney, “Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings,”
Advanced Drug Discovery Rev
.
46
, No. 1-3, 3–26 (2001).
J. R. Krumrine, A. T. Maynard, and C. L. Lerman, “Statistical Tools for Virtual Screening,”
J. Medicin. Chem.
48
, No. 23, 7477 (2005).
C. Bissantz, G. Folkers, and D. Rognan, “Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations,”
J. Medicin. Chem.
43
, No. 25, 4759–4767 (2000).
M. Stahl and M. Rarey, “Detailed Analysis of Scoring Functions for Virtual Screening,”
J. Medicin. Chem.
44
, No. 7, 1035–1042 (2001).
M. Vieth, J. D. Hirst, A. Kolinski, and C. L. Brooks, “Assessing Energy Functions for Flexible Docking,”
J. Comput. Chem.
19
, No. 14, 1612–1622 (1998).
J. R. Schames, R. H. Henchman, J. S. Siegel, C. A. Sotriffer, H. Ni, and J. A. McCammon, “Discovery of a Novel Binding Trench in HIV Integrase,”
J. Medicin. Chem.
47
, No. 8, 1879–1881 (2004).
O. Guner, O. Clement, and Y. Kurogi, “Pharmacophore Modeling and Three Dimensional Database Searching for Drug Design Using Catalyst: Recent Advances,”
Current Medicin. Chem.
11
, No. 22, 2991–3005 (2004).
G. Jones, P. Willett, R. C. Glen, A. R. Leach, and R. Taylor, “Development and Validation of a Genetic Algorithm for Flexible Docking,”
J. Mol. Biol.
267
, No. 3, 727–748 (1997).
B. Kramer, M. Rarey, and T. Lengauer, “Evaluation of the FLEXX Incremental Construction Algorithm for Protein–Ligand Docking,”
Proteins: Structure, Function, and Bioinformatics
37
, No. 2, 228–241 (1999).
T. J. A. Ewing, S. Makino, A. G. Skillman, and I. D. Kuntz, “DOCK 4.0: Search Strategies for Automated Molecular Docking of Flexible Molecule Databases,”
Computer Aided Mol. Design
15
, No. 5, 411–428 (2001).
D. S. Goodsell, G. M. Morris, and A. J. Olson, “Automated Docking of Flexible Ligands: Applications of AutoDock,”
Computer Aided Mol. Design
9
, No. 1, 1–5 (1996).
R. A. Friesner, J. L. Banks, R. B. Murphy, T. A. Halgren, J. J. Klicic, D. T. Mainz, M. P. Repasky, E. H. Knoll, M. Shelley, and J. K. Perry, “Glide: A New Approach For Rapid, Accurate Docking And Scoring. 1. Method and Assessment of Docking Accuracy,”
J. Medicin. Chem
.
47
, No. 7, 1739–1749 (2004).
T. A. Halgren, R. B. Murphy, R. A. Friesner, H. S. Beard, L. L. Frye, W. T. Pollard, and J. L. Banks, “Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening,”
J. Medicin. Chem.
47
, No. 7, 1750–1759 (2004).
R. Abagyan, M. Totrov, and D. Kuznetsov, “ICM—A New Method for Protein Modeling and Design: Applications to Docking and Structure Prediction from the Distorted Native Conformation,”
J. Comput. Chem.
15
, No. 5, 488–506 (1994).
M. Vieth, J. D. Hirst, B. N. Dominy, H. Daigler, and C. L. Brooks, “Assessing Search Strategies for Flexible Docking,”
J. Comput. Chem.
16
, No. 14, 1623–1631 (1998).
R. Rosenfeld, S. Vajda, and C. DeLisi, “Flexible Docking and Design,”
Biophysics Biomol. Structure
24
, No. 1, 677–700 (1995).
I. Muegge and Y. C. Martin, “A General and Fast Scoring Function for Protein–Ligand Interactions: A Simplified Potential Approach,”
J. Medicin. Chem.
42
, No. 5, 791–804 (1999).
M. Jacobsson, P. Liden, E. Stjernschantz, H. Bostrom, and U. Norinder, “Improving Structure-Based Virtual Screening by Multivariate Analysis of Scoring Data,”
J. Medicin. Chem.
46
, No. 26, 5781–5789 (2003).
R. Wang, Y. Lu, and S. Wang, “Comparative Evaluation of 11 Scoring Functions for Molecular Docking,”
J. Medicin. Chem.
46
, No. 12, 2287–2303 (2003).
J. W. Raymond, M. Jalaie, and M. P. Bradley, “Conditional Probability: A New Fusion Method for Merging Disparate Virtual Screening Results,”
J. Chem. Information Comput. Sci.
44
, No. 2, 601–609 (2004).
M. Feher, “Consensus Scoring for Protein–Ligand Interactions,”
Drug Discovery Today
11
, No. 9-10, 421–428 (2006).
J. M. Yang, Y. F. Chen, T. W. Shen, B. S. Kristal, and D. F. Hsu, “Consensus Scoring Criteria for Improving Enrichment in Virtual Screening,”
J. Chem. Information Modeling
45
, No. 4, 1134–1146 (2005).
M. A. Miteva, W. H. Lee, M. O. Montes, and B. O. Villoutreix, “Fast Structure-Based Virtual Ligand Screening Combining FRED, DOCK, and Surflex,”
J. Medicin. Chem.
48
, No. 19, 6012 (2005).
M. L. Verdonk, V. Berdini, M. J. Hartshorn, W. T. M. Mooij, C. W. Murray, R. D. Taylor, and P. Watson, “Virtual Screening Using Protein–Ligand Docking: Avoiding Artificial Enrichment,”
J. Chem. Information Comput. Sci.
44
, No. 3, 793–806 (2004).
L. Xing, E. Hodgkin, Q. Liu, and D. Sedlock, “Evaluation and Application of Multiple Scoring Functions for a Virtual Screening Experiment,”
J. Computer Aided Mol. Design
18
, No. 5, 333–344 (2004).
D. W. Zhang, Y. Xiang, A. M. Gao, and J. Z. H. Zhang, “Quantum Mechanical Map for Protein–Ligand Binding with Application to
β
-Trypsin/Benzamidine Complex,”
J. Chem. Physics
120
, No. 3, 1145–1148 (2004).
T. Xiang, F. Liu, and D. M. Grant, “Stochastic Dynamics of n-Nonane and Related Molecules in Solution Compared with Nuclear Magnetic Resonance Coupled Relaxation Times,”
J. Chem. Physics
95
, No. 10, 7576–7590 (2005).
K. Raha and K. M. Merz, Jr., “Large-Scale Validation of a Quantum Mechanics Based Scoring Function: Predicting the Binding Affinity and the Binding Mode of a Diverse Set of Protein–Ligand Complexes,”
J. Medicin. Chem.
48
, No. 14, 4558–4575 (2005).
H. J. Woo and B. Roux, “Calculation of Absolute Protein–Ligand Binding Free Energy from Computer Simulations,”
Proc. Natl. Acad. Sci.
102
, No. 19, 6825–6830 (2005).
H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne, “The Protein Data Bank,”
Nucleic Acids Res.
28
, No. 1, 235–242 (2000).
J. Bajorath, “Integration of Virtual and High-Throughput Screening,”
Nat. Rev. Drug Discovery
1
, No. 11, 882–894 (2002).
B. Waszkowycz, T. D. J. Perkins, R. A. Sykes, and J. Li,
“Large-Scale Virtual Screening for Discovering Leads in the Postgenomic Era,”
IBM Syst. J.
40
, No. 2, 360–378 (2001).
G. L.-T. Chiu, M. Gupta, and A. K. Royyuru,
“Preface,”
IBM J. Res. & Dev.
49
, No. 2/3, 191–194 (2005).
P. A. Boyle, D. Chen, N. H. Christ, M. A. Clark, S. D. Cohen, C. Cristian, Z. Dong, et al.,
“Overview of the QCDSP and QCDOC Computers,”
IBM J. Res. & Dev.
49
, No. 2/3, 351–365 (2005).
J. M. Bull, A. Gray, J. Hein, and L. Smith, “Application Performance of the Blue Gene Architecture,”
Proceedings of the 2006 ACM/IEEE Conference on Supercomputing
(tutorial), Tampa, FL, 2006.
S. Wu, I. McNae, G. Kontopidis, S. McClue, C. McInnes, K. Stewart, S. Wang, et al., “Discovery of a Novel Family of CDK Inhibitors with the Program LIDAEUS: Structural Basis for Ligand-Induced Disordering of the Activation Loop,”
Structure
11
, No. 12, 1537–1546 (2003).
P. Taylor, E. Blackburn, Y. Sheng, S. Harding, K. Hsin, K. Kan, S. Shave, and M. D. Walkinshaw, “Ligand Discovery and Virtual Screening Using the Program LIDAEUS,”
Br. J. Pharmacol.,
in press.
P. K. Weiner and P. A. Kollman, “AMBER: Assisted Model Building with Energy Refinement. A General Program for Modeling Molecules and Their Interactions,”
J. Comput. Chem.
2
, No. 3, 287–303 (1981).
“The
openMosix
Project,” 2007; see
http://openmosix.sourceforge.net/
.
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