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Letter

Quality Assurance for Biomolecular Simulations

Stuart E. Murdock,^†^# Kaihsu Tai,*^§ Muan Hong Ng,^‡ Steven Johnston,^‡ Bing Wu,^§ Hans Fangohr,^‡ Charles A. Laughton, Jonathan W. Essex,*^† and Mark S. P. Sansom^§

J. Chem. Theory Comput., 2006, 2 (6), pp 1477–1481

DOI: 10.1021/ct6001708

Publication Date (Web): October 3, 2006

†

School of Chemistry, University of Southampton.

Current address: Schrödinger Inc., 101 SW Main Street, Suite 1300, Portland, OR 97204.

Corresponding author phone: +44 23 80592794; e-mail: j.w.essex@ soton.ac.uk (J.W.E.) and e-mail: kaihsu.tai@bioch.ox.ac.uk (K.T.).

Department of Biochemistry, University of Oxford.

‡

School of Engineering Sciences, University of Southampton.

Oxford e-Science Centre, University of Oxford.

University of Nottingham.

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 simulationsfor example BioSimGrid (http://www.biosimgrid.org/)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.