title: MrGrid: a portable grid based molecular replacement pipeline.
abstract: BACKGROUND
  The crystallographic determination of protein structures can be computationally demanding and for difficult cases can benefit from user-friendly interfaces to high-performance computing resources. Molecular replacement (MR) is a popular protein crystallographic technique that exploits the structural similarity between proteins that share some sequence similarity. But the need to trial permutations of search models, space group symmetries and other parameters makes MR time- and labour-intensive. However, MR calculations are embarrassingly parallel and thus ideally suited to distributed computing. In order to address this problem we have developed MrGrid, web-based software that allows multiple MR calculations to be executed across a grid of networked computers, allowing high-throughput MR.
  
  
  RESULTS
  MrGrid is a portable web based application written in Java/JSP and Ruby, and taking advantage of Apple Xgrid technology. Designed to interface with a user defined Xgrid resource the package manages the distribution of multiple MR runs to the available nodes on the Xgrid. We evaluated MrGrid using 10 different protein test cases on a network of 13 computers, and achieved an average speed up factor of 5.69.
  
  
  CONCLUSIONS
  MrGrid enables the user to retrieve and manage the results of tens to hundreds of MR calculations quickly and via a single web interface, as well as broadening the range of strategies that can be attempted. This high-throughput approach allows parameter sweeps to be performed in parallel, improving the chances of MR success.
authors.affiliation: Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Jason W
authors.initials: JW
authors.lastname: Schmidberger
authors.forename: Mark A
authors.initials: MA
authors.lastname: Bate
authors.forename: Cyril F
authors.initials: CF
authors.lastname: Reboul
authors.forename: Steve G
authors.initials: SG
authors.lastname: Androulakis
authors.forename: Jennifer M N
authors.initials: JM
authors.lastname: Phan
authors.forename: James C
authors.initials: JC
authors.lastname: Whisstock
authors.forename: Wojtek J
authors.initials: WJ
authors.lastname: Goscinski
authors.forename: David
authors.initials: D
authors.lastname: Abramson
authors.forename: Ashley M
authors.initials: AM
authors.lastname: Buckle
mesh_terms: D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D020407:Internet; D011381:Programming Languages; D011506:Proteins / Q000737:chemistry; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins
references.citation: Methods Enzymol. 2003;374:229-44
references.pmid: 14696376
references.citation: Acta Crystallogr D Biol Crystallogr. 1997 May 1;53(Pt 3):240-55
references.pmid: 15299926
references.citation: Protein Sci. 2003 Sep;12(9):2001-14
references.pmid: 12930999
references.citation: J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674
references.pmid: 19461840
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W284-8
references.pmid: 15980471
references.citation: J Mol Biol. 1995 Apr 7;247(4):536-40
references.pmid: 7723011
references.citation: Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):760-3
references.pmid: 15299374
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Protein Sci. 2006 May;15(5):1187-92
references.pmid: 16597838