title: MolProbity for the masses-of data.
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.
authors.affiliation: National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA.
authors.forename: Vincent B
authors.initials: VB
authors.lastname: Chen
authors.affiliation: BioMagResBank, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA.
authors.forename: Jonathan R
authors.initials: JR
authors.lastname: Wedell
authors.affiliation: BioMagResBank, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA.
authors.forename: R Kent
authors.initials: RK
authors.lastname: Wenger
authors.affiliation: BioMagResBank, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA.
authors.forename: Eldon L
authors.initials: EL
authors.lastname: Ulrich
authors.affiliation: National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA. markley@nmrfam.wisc.edu.
authors.forename: John L
authors.initials: JL
authors.lastname: Markley
mesh_terms: D009682:Magnetic Resonance Spectroscopy; D009696:Nucleic Acids / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012984:Software; D013223:Statistics as Topic
chemical_list: D009696:Nucleic Acids; D011506:Proteins
keywords: BioMagResBank (BMRB); HTCondor; High-throughput computing; MolProbity; Protein Data Bank; Structure validation