Molecular Structure Determination on the Grid

Grids represent an emerging technology that allows geographicallyand organizationally-distributed resources (e.g., compute systems, data repositories, sensors, imaging systems, and so forth) to be linked in a fashion that is transparent to the user. A state-of-the-art grid presents a ubiquitous set of resources to a user. The New York State Grid (NYS Grid) is an integrated computational and data grid that provides access to users from around the world to a wide variety of resources. This Grid can be accessed via a Web portal, where the users have access to their data sets and applications, but do not need to be made aware of the details of the data storage or computational devices that are specifically employed in solving their problems. Grid-enabled versions of the SnB and BnP programs, which implement the Shake-and-Bake method of molecular structure (SnB) and substructure (BnP) determination, respectively, have been deployed on NYS Grid. Further, through the Grid Portal, SnB has been run simultaneously on all computational resources on NYS Grid as well as on more than 1100 of the over 3000 processors available through the Open Science Grid.

[1]  Steven M. Gallo,et al.  SnB: crystal structure determination via shake-and-bake , 1994 .

[2]  R Miller,et al.  Structure solution by minimal-function phase refinement and Fourier filtering. I. Theoretical basis. , 1994, Acta crystallographica. Section A, Foundations of crystallography.

[3]  G. Sheldrick.  Phase annealing in SHELX-90: direct methods for larger structures , 1990 .

[4]  Carmelo Ragusa.  Business Grids, Infrastructuring the Future of ICT , 2010 .

[5]  Antonio Liotta,et al.  Handbook of Research on P2P and Grid Systems for Service-oriented Computing: Models, Methodologies a , 2010 .

[6]  David E. Keyes,et al.  Proceedings of the Sixth SIAM Conference on Parallel Processing for Scientific Computing, PPSC 1993, Norfolk, Virginia, USA, March 22-24, 1993 , 1993, PPSC.

[7]  Brijesh Kumar Chaurasia,et al.  Mechanism for Privacy Preservation in VANETS , 2010, Int. J. Grid High Perform. Comput..

[8]  Russ Miller,et al.  The design and implementation of SnB version 2.0 , 1999 .

[9]  Russ Miller,et al.  Grid-based research, development, and deployment in New York State , 2008, 2008 IEEE International Symposium on Parallel and Distributed Processing.

[10]  Deo Prakash Vidyarthi,et al.  A Security Prioritized Computational Grid Scheduling Model: An Analysis , 2009, Int. J. Grid High Perform. Comput..

[11]  Maria Cristina Burla,et al.  SIR88 – a direct‐methods program for the automatic solution of crystal structures , 1989 .

[12]  Na Helian,et al.  Predictive File Replication on the Data Grids , 2010, Int. J. Grid High Perform. Comput..

[13]  Tsuyoshi Inoue,et al.  Structure of E. coli ketopantoate hydroxymethyl transferase complexed with ketopantoate and Mg2+, solved by locating 160 selenomethionine sites. , 2003, Structure.

[14]  Manolis Tsiknakis,et al.  Computational Methods and Tools for Decision Support in Biomedicine: An Overview of Algorithmic Challenges , 2009 .

[15]  M. R. van Steen,et al.  Enforcing Fairness in Asynchronous Collaborative Environments , 2010 .

[16]  Russ Miller,et al.  On the application of parallel genetic algorithms in X-ray crystallography , 1994, Proceedings of IEEE Scalable High Performance Computing Conference.

[17]  T. Debaerdemaeker,et al.  On the application of phase relationships to complex structures. XXIV. The Sayre tangent formula , 1985 .

[18]  Robert H. Blessing,et al.  Towards automated protein structure determination: BnP, the SnB-PHASES interface , 2002 .

[19]  Ankur Gupta,et al.  Toward a Quality-of-Service Framework for Peer-to-Peer Applications , 2010, Int. J. Distributed Syst. Technol..

[20]  Jack Dongarra,et al.  Handbook of Research on Scalable Computing Technologies , 2009 .

[21]  Russ Miller,et al.  Molecular structure determination on a computational and data grid , 2004, Parallel Comput..

[22]  H. Hauptman,et al.  A theory of phase determination for the four types of non-centrosymmetric space groups 1P222, 2P22, 3P12, 3P22 , 1956 .

[23]  R. Miller,et al.  Solving the Phase Problem of X-Ray Crystallography on Parallel Machines , 1993, PPSC.

[24]  Russ Miller,et al.  A Client-Server Prototype For Grid-Enabling Application Template Design , 2004, Parallel Process. Lett..

[25]  R Miller,et al.  Structure solution by minimal-function phase refinement and Fourier filtering. II. Implementation and applications. , 1994, Acta crystallographica. Section A, Foundations of crystallography.

[26]  Li Qi,et al.  Dynamic Maintenance in ChinaGrid Support Platform , 2011 .

[27]  Valentin Cristea,et al.  Bio-Inspired Techniques for Resources State Prediction in Large Scale Distributed Systems , 2011, Int. J. Distributed Syst. Technol..

[28]  Frank Z. Wang,et al.  Handbook of Research on Grid Technologies and Utility Computing: Concepts for Managing Large-Scale Applications , 2009 .

[29]  Robert H. Blessing,et al.  Difference structure‐factor normalization for heavy‐atom or anomalous‐scattering substructure determinations , 1999 .

[30]  Oberer Eselsberg.  On the Application of Phase Relationships to Complex Structures. XXIV. The Sayre Tangent Formula , 2001 .

[31]  Russ Miller,et al.  Evolutionary molecular structure determination using Grid-enabled data mining , 2004, IEEE International Symposium on Cluster Computing and the Grid, 2004. CCGrid 2004..

[32]  Francine Berman,et al.  Grid Computing: Making the Global Infrastructure a Reality , 2003 .

[33]  Dhabaleswar K. Panda,et al.  Data intensive computing , 2006, SC.

[34]  S. Ealick,et al.  The crystal structure of ADP-L-glycero-D-mannoheptose 6-epimerase: catalysis with a twist. , 2000, Structure.

[35]  Sourav Mukhopadhyay,et al.  Adaptive Routing Strategy for Large Scale Rearrangeable Symmetric Networks , 2010, Int. J. Grid High Perform. Comput..

[36]  George Sheldrick,et al.  Ab initio structure solution of a dimeric cytochrome c 3 from Desulfovibrio gigas containing disulfide bridges , 1999, JBIC Journal of Biological Inorganic Chemistry.

[37]  A. K. Bhuiya,et al.  The refinement of atomic parameters by direct calculation of the minimum residual , 1963 .

[38]  Haruki Nakamura,et al.  Announcing the worldwide Protein Data Bank , 2003, Nature Structural Biology.

[39]  H. Hauptman,et al.  On the application of the minimal principle to solve unknown structures. , 1993, Science.

[40]  Russ Miller,et al.  Evolutionary molecular structure determination using grid-enabled data mining , 2004, Parallel Comput..

[41]  Martins Innus,et al.  SnB version 2.2: an example of crystallographic multiprocessing , 2002 .

[42]  R Miller,et al.  Application of the minimal principle to peptide structures. , 1993, Acta crystallographica. Section D, Biological crystallography.

[43]  Yong Meng Teo,et al.  Hierarchical Structured Peer-to-Peer Networks , 2010 .

[44]  George M Sheldrick,et al.  Substructure solution with SHELXD. , 2002, Acta crystallographica. Section D, Biological crystallography.

[45]  W Furey,et al.  PHASES-95: a program package for processing and analyzing diffraction data from macromolecules. , 1997, Methods in enzymology.

[46]  Ami Marowka,et al.  The GRID: Blueprint for a New Computing Infrastructure , 2000, Parallel Distributed Comput. Pract..