Protein simulation data in the relational model

Journal of Supercomputing

Volumn 62, Issue 1, 2012, Pages 150-173

  Simms, Andrew M ^a   Daggett, Valerie ^a,b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b University of Washington   (United States)

Author keywords

Data warehouse; Relational database

Indexed keywords

DESIGN EFFORT; DIMENSIONAL DESIGN; HIGH PERFORMANCE COMPUTING; MOLECULAR DYNAMICS SIMULATIONS; PROTEIN SIMULATIONS; RELATIONAL DATABASE; RELATIONAL MODEL; SCALABLE MODEL; SCIENTIFIC DATA; SIMULATION SOFTWARE; SQL SERVERS;

COMPUTER SOFTWARE; DATA WAREHOUSES; MOLECULAR DYNAMICS;

COMPUTER SIMULATION;

EID: 84865662866     PISSN: 09208542     EISSN: 15730484     Source Type: Journal    
DOI: 10.1007/s11227-011-0692-3     Document Type: Article

References (18)

1. EF Codd 1970 A relational model of data for large shared data banks Commun ACM 13 377 387 0207.18003 10.1145/362384.362685
2. Codd EF, Codd SB et al (1993) Providing OLAP to user-analysts: an IT mandate
3. HM Berman J Westbrook, et al. 2000 The protein data bank Nucleic Acids Res 28 235 242 10.1093/nar/28.1.235 (Pubitemid 30047768)
4. K Henrick Z Feng, et al. 2008 Remediation of the protein data bank archive Nucleic Acids Res 36 D426-33 (Pubitemid 351149761)
5. AM Simms RD Toofanny C Kehl NC Benson V Daggett 2008 Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations Protein Eng Des Sel 21 369 377 10.1093/protein/gzn012 (Pubitemid 351786655)
6. RD Schaeffer AL Jonsson AM Simms V Daggett 2011 Generation of a consensus protein domain dictionary Bioinformatics 27 46 54 10.1093/bioinformatics/btq625
7. Simms AM, Beck DAC, Jonsson AL, Schaeffer RD, Daggett V (2011) The molecular mechanics parameter markup language (submitted for publication)
8. Beck DAC, Alonso DOV, Daggett V (2000-2011) in lucem molecular mechanics (ilmm)
9. RD Toofanny AM Simms DAC Beck V Daggett 2011 Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection BMC Bioinform 12 334 10.1186/1471-2105-12-334
10. M Levitt 1983 Molecular dynamics of native protein. I. Computer simulation of trajectories J Mol Biol 168 595 617 10.1016/S0022-2836(83)80304-0
11. M Levitt M Hirshberg R Sharon V Daggett 1995 Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution Comput Phys Commun 91 215 231 10.1016/0010-4655(95)00049-L
12. Microsoft Corporation (2007) SQL server 2008
13. International Organization for Standardization, International Electrotechnical Commission (2001) Information technology: database languages: SQL. Part 1, Framework (SQL/framework). Geneva
14. Microsoft Corporation (2010) SQL Server Books Online
15. Fritchey G, Dam S (2009) SQL server 2008 query performance tuning distilled. New York
16. IEEE Computer Society Standards Committee, IEEE Standards Board et al (1985) IEEE standard for binary floating-point arithmetic
17. CE Kehl AM Simms RD Toofanny V Daggett 2008 Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data Protein Eng Des Sel 21 379 386 10.1093/protein/gzn015 (Pubitemid 351786657)
18. Simms AM, Daggett V (2011) (in preparation)