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PubMed · 14646078

Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service.

Vinod Reddy·Stanley M Swanson·Brent Segelke·Katherine A Kantardjieff·James C Sacchettini·Bernhard Rupp
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Abstract

Anticipating a continuing increase in the number of structures solved by molecular replacement in high-throughput crystallography and drug-discovery programs, a user-friendly web service for automated molecular replacement, map improvement, bias removal and real-space correlation structure validation has been implemented. The service is based on an efficient bias-removal protocol, Shake&wARP, and implemented using EPMR and the CCP4 suite of programs, combined with various shell scripts and Fortran90 routines. The service returns improved maps, converted data files and real-space correlation and B-factor plots. User data are uploaded through a web interface and the CPU-intensive iteration cycles are executed on a low-cost Linux multi-CPU cluster using the Condor job-queuing package. Examples of map improvement at various resolutions are provided and include model completion and reconstruction of absent parts, sequence correction, and ligand validation in drug-target structures.

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Apolipoproteins EBacterial ProteinsBenzimidazolesBotulinum ToxinsCalmodulinCarbohydrate EpimerasesCarboxy-LyasesClostridium botulinumCluster AnalysisCrystallography, X-RayDatabases, GeneticDatabases, ProteinEndopeptidasesGenomicsInternetMembrane ProteinsModels, MolecularMycobacterium tuberculosisProtein ConformationR-SNARE ProteinsStatic ElectricityCarbohydrate DehydrogenasesJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, P.H.S.

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Vinod Reddy, Stanley M Swanson, Brent Segelke, Katherine A Kantardjieff, James C Sacchettini, Bernhard Rupp. 2003-11-27. Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service.. https://doi.org/10.1107/s0907444903020316

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