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Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB
Vinod Reddy1, Stanley M Swanson, Brent Segelke
1Biochemistry and Biophysics Department, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA.
Acta Crystallographica. Section D, Biological Crystallography
|December 4, 2003
Summary
A new web service automates molecular replacement and map improvement for crystallography, enhancing drug discovery. This tool aids in completing models and validating ligands in complex structures.
Area of Science:
- Structural biology
- Computational crystallography
- Drug discovery
Background:
- High-throughput crystallography is increasingly used for structure determination.
- Automated methods are needed to streamline molecular replacement and map improvement.
Purpose of the Study:
- To develop a user-friendly web service for automated molecular replacement and map improvement.
- To provide tools for bias removal and structure validation in crystallographic studies.
Main Methods:
- The service utilizes the Shake&wARP protocol for bias removal.
- It integrates EPMR, CCP4 suite, shell scripts, and Fortran90 routines.
- Web interface for data upload and a Linux cluster with Condor for computation.
Main Results:
- Improved electron density maps with model completion and correction.
- Enhanced validation through real-space correlation and B-factor plots.
- Successful application in drug-target structure analysis and ligand validation.
Conclusions:
- The implemented web service offers an efficient solution for automated molecular replacement and map enhancement.
- It supports various aspects of structure analysis, including model building and ligand validation.
- The service is valuable for high-throughput crystallography and drug discovery programs.