title: Quality Assurance for Biomolecular Simulations.
abstract: Contemporary structural biology has an increased emphasis on high-throughput methods. Biomolecular simulations can add value to structural biology via the provision of dynamic information. However, at present there are no agreed measures for the quality of biomolecular simulation data. In this Letter, we suggest suitable measures for the quality assurance of molecular dynamics simulations of biomolecules. These measures are designed to be simple, fast, and general. Reporting of these measures in simulation papers should become an expected practice, analogous to the reporting of comparable quality measures in protein crystallography. We wish to solicit views and suggestions from the simulation community on methods to obtain reliability measures from molecular-dynamics trajectories. In a database which provides access to previously obtained simulations [Formula: see text] for example BioSimGrid ( http://www.biosimgrid.org/ ) [Formula: see text] the user needs to be confident that the simulation trajectory is suitable for further investigation. This can be provided by the simulation quality measures which a user would examine prior to more extensive analyses.
authors.affiliation: School of Chemistry and School of Engineering Sciences, University of Southampton, United Kingdom, Department of Biochemistry and Oxford e-Science Centre, University of Oxford, United Kingdom, and School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, United Kingdom.
authors.forename: Stuart E
authors.initials: SE
authors.lastname: Murdock
authors.affiliation: School of Chemistry and School of Engineering Sciences, University of Southampton, United Kingdom, Department of Biochemistry and Oxford e-Science Centre, University of Oxford, United Kingdom, and School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, United Kingdom.
authors.forename: Kaihsu
authors.initials: K
authors.lastname: Tai
authors.affiliation: School of Chemistry and School of Engineering Sciences, University of Southampton, United Kingdom, Department of Biochemistry and Oxford e-Science Centre, University of Oxford, United Kingdom, and School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, United Kingdom.
authors.forename: Muan Hong
authors.initials: MH
authors.lastname: Ng
authors.affiliation: School of Chemistry and School of Engineering Sciences, University of Southampton, United Kingdom, Department of Biochemistry and Oxford e-Science Centre, University of Oxford, United Kingdom, and School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, United Kingdom.
authors.forename: Steven
authors.initials: S
authors.lastname: Johnston
authors.affiliation: School of Chemistry and School of Engineering Sciences, University of Southampton, United Kingdom, Department of Biochemistry and Oxford e-Science Centre, University of Oxford, United Kingdom, and School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, United Kingdom.
authors.forename: Bing
authors.initials: B
authors.lastname: Wu
authors.affiliation: School of Chemistry and School of Engineering Sciences, University of Southampton, United Kingdom, Department of Biochemistry and Oxford e-Science Centre, University of Oxford, United Kingdom, and School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, United Kingdom.
authors.forename: Hans
authors.initials: H
authors.lastname: Fangohr
authors.affiliation: School of Chemistry and School of Engineering Sciences, University of Southampton, United Kingdom, Department of Biochemistry and Oxford e-Science Centre, University of Oxford, United Kingdom, and School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, United Kingdom.
authors.forename: Charles A
authors.initials: CA
authors.lastname: Laughton
authors.affiliation: School of Chemistry and School of Engineering Sciences, University of Southampton, United Kingdom, Department of Biochemistry and Oxford e-Science Centre, University of Oxford, United Kingdom, and School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, United Kingdom.
authors.forename: Jonathan W
authors.initials: JW
authors.lastname: Essex
authors.affiliation: School of Chemistry and School of Engineering Sciences, University of Southampton, United Kingdom, Department of Biochemistry and Oxford e-Science Centre, University of Oxford, United Kingdom, and School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, United Kingdom.
authors.forename: Mark S P
authors.initials: MS
authors.lastname: Sansom