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

Acta Crystallogr D Biol Crystallogr. 2003 Dec;59(Pt 12):2200-10. doi: 10.1107/s0907444903020316. Epub 2003 Nov 27.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Apolipoproteins E / chemistry
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Benzimidazoles / chemistry
  • Botulinum Toxins / chemistry
  • Calmodulin / chemistry
  • Carbohydrate Epimerases / chemistry
  • Carboxy-Lyases / chemistry
  • Clostridium botulinum / chemistry
  • Cluster Analysis
  • Crystallography, X-Ray / methods*
  • Databases, Genetic*
  • Databases, Protein*
  • Endopeptidases / chemistry
  • Genomics
  • Internet*
  • Membrane Proteins / chemistry
  • Models, Molecular
  • Mycobacterium tuberculosis / enzymology
  • Mycobacterium tuberculosis / genetics
  • Protein Conformation
  • R-SNARE Proteins
  • Static Electricity

Substances

  • Apolipoproteins E
  • Bacterial Proteins
  • Benzimidazoles
  • Calmodulin
  • Membrane Proteins
  • R-SNARE Proteins
  • bis(5-amidino-2-benzimidazolyl)methane
  • Endopeptidases
  • Botulinum Toxins
  • Carboxy-Lyases
  • Carbohydrate Epimerases
  • dTDP-4-ketorhamnose 3,5-epimerase