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

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.

author list (cited authors)

  • Reddy, V., Swanson, S., Segelke, B., Kantardjieff, K. A., Sacchettini, J. C., & Rupp, B.

citation count

  • 40

complete list of authors

  • Reddy, Vinod||Swanson, Stanley M||Segelke, Brent||Kantardjieff, Katherine A||Sacchettini, James C||Rupp, Bernhard

publication date

  • November 2003