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MolProbity for the masses-of data.
Vincent B Chen1, Jonathan R Wedell2, R Kent Wenger2
1National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA.
Journal of Biomolecular NMR
|July 22, 2015
Summary
A new high-throughput version of MolProbity (MolProbity-HTC) enables rapid validation of large protein and nucleic acid structure datasets. This tool accelerates structural analysis and quality assessment for databases like the Protein Data Bank (PDB).
Area of Science:
- Structural Biology
- Computational Biology
- Bioinformatics
Background:
- MolProbity is a key software for validating protein and nucleic acid structures.
- Existing MolProbity scripts are inefficient for large-scale structure dataset validation.
Purpose of the Study:
- To develop a high-throughput version of MolProbity (MolProbity-HTC) for efficient analysis of large structure datasets.
- To enable longitudinal analysis of structural data from repositories like the PDB and theoretical computations.
Main Methods:
- Utilized HTCondor software to create a high-throughput computing cluster version of MolProbity.
- Implemented MolProbity-HTC to overcome limitations of single-structure analysis.
- Applied MolProbity-HTC to validate the entire Protein Data Bank (PDB).
Main Results:
- MolProbity-HTC significantly accelerates the validation of large structural datasets.
- The entire PDB was successfully validated using MolProbity-HTC.
- A new visual quality chart was developed for the BioMagResBank website.
Conclusions:
- MolProbity-HTC provides a scalable solution for large-scale structural validation.
- The new visualization tool enhances user accessibility to structural quality information for NMR ensembles.
- This advancement facilitates more efficient and comprehensive structural data analysis.
Keywords:
BioMagResBank (BMRB)HTCondorHigh-throughput computingMolProbityProtein Data BankStructure validationMore Related Videos
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