Abstract
MolProbity is a powerful software program for validating structures of proteins and nucleic acids. Although MolProbity includes scripts for batch analysis of structures, because these scripts analyze structures one at a time, they are not well suited for the validation of a large dataset of structures. We have created a version of MolProbity (MolProbity-HTC) that circumvents these limitations and takes advantage of a high-throughput computing cluster by using the HTCondor software. MolProbity-HTC enables the longitudinal analysis of large sets of structures, such as those deposited in the PDB or generated through theoretical computation—tasks that would have been extremely time-consuming using previous versions of MolProbity. We have used MolProbity-HTC to validate the entire PDB, and have developed a new visual chart for the BioMagResBank website that enables users to easily ascertain the quality of each model in an NMR ensemble and to compare the quality of those models to the rest of the PDB.
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Acknowledgments
We thank Miron Livny for helpful and lively discussions about the use of HTCondor. We also thank Dimitri Maziuk for technical assistance and help with systems administration at the BMRB, and W. Milo Westler for discussions about NMR methodology. This work was supported by NIH Grants R01 GM109046 and P41GM103399. VBC has received partial support from NLM Grant 5T15LM007359.
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Chen, V.B., Wedell, J.R., Wenger, R.K. et al. MolProbity for the masses–of data. J Biomol NMR 63, 77–83 (2015). https://doi.org/10.1007/s10858-015-9969-9
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DOI: https://doi.org/10.1007/s10858-015-9969-9