Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service.
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.
Reddy
Vinod
V
Biochemistry and Biophysics Department, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA.
Swanson
Stanley M
SM
Segelke
Brent
B
Kantardjieff
Katherine A
KA
Sacchettini
James C
JC
Rupp
Bernhard
B
D001057:Apolipoproteins E / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D001562:Benzimidazoles / Q000737:chemistry; D001905:Botulinum Toxins / Q000737:chemistry; D002147:Calmodulin / Q000737:chemistry; D002238:Carbohydrate Epimerases / Q000737:chemistry; D002262:Carboxy-Lyases / Q000737:chemistry; D003014:Clostridium botulinum / Q000737:chemistry; D016000:Cluster Analysis; D018360:Crystallography, X-Ray / Q000379:methods*; D030541:Databases, Genetic; D030562:Databases, Protein; D010450:Endopeptidases / Q000737:chemistry; D023281:Genomics; D020407:Internet; D008565:Membrane Proteins / Q000737:chemistry; D008958:Models, Molecular; D009169:Mycobacterium tuberculosis / Q000201:enzymology / Q000235:genetics; D011487:Protein Conformation; D050683:R-SNARE Proteins; D055672:Static Electricity; D002237:Carbohydrate Dehydrogenases
D001057:Apolipoproteins E; D001426:Bacterial Proteins; D001562:Benzimidazoles; D001905:Botulinum Toxins; D002147:Calmodulin; D002238:Carbohydrate Epimerases; D002262:Carboxy-Lyases; D010450:Endopeptidases; D008565:Membrane Proteins; D050683:R-SNARE Proteins; C025426:bis(5-amidino-2-benzimidazolyl)methane; C020092:dTDP-4-ketorhamnose 3,5-epimerase; D002237:Carbohydrate Dehydrogenases