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Parmbsc1: a refined force field for DNA simulations

Nature Methods volume 13, pages 55–58 (2016)Cite this article

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Abstract

We present parmbsc1, a force field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (representing a total simulation time of ∼140 μs) covering most of DNA structural space. Parmbsc1 provides high-quality results in diverse systems. Parameters and trajectories are available at http://mmb.irbbarcelona.org/ParmBSC1/.

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Figure 1: Analysis of the DDD.
Figure 2: Analysis of noncanonical DNA structures.
Figure 3: Analysis of DNA-protein complexes.

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Acknowledgements

M.O. thanks the Spanish Ministry of Science (BIO2012-32868), the Catalan SGR, the Instituto Nacional de Bioinformática and the European Research Council (ERC SimDNA) for support. M.O. is an academia researcher in the Catalan Institution for Research and Advanced Studies (ICREA). M.O. thanks the Barcelona Supercomputing Center for CPU and GPU time on MareNostrum and MinoTauro. C.A.L., S.A.H. and A.N. thank the UK HECBioSim Consortium for time on the ARCHER high-performance computing system (grant EP-L000253-1). A.N. was supported by the Biotechnology and Biological Sciences Research Council (BBSRC; grant BB-I019294-1) and thanks ARC Leeds for computational resources. P.D.D. is a PEDECIBA (Programa de Desarrollo de las Ciencias Básicas) and SNI (Sistema Nacional de Investigadores; ANII, Uruguay) researcher. D.A.C. thanks C. Liu for assistance with the crystal simulation analysis.

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Authors and Affiliations

  1. Institute for Research in Biomedicine (IRB) Barcelona, the Barcelona Institute of Science and Technology, Barcelona, Spain

    Ivan Ivani, Pablo D Dans, Ignacio Faustino, Adam Hospital, Jürgen Walther, Alexandra Balaceanu, Guillem Portella, Federica Battistini & Modesto Orozco

  2. Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain

    Ivan Ivani, Pablo D Dans, Ignacio Faustino, Adam Hospital, Jürgen Walther, Pau Andrio, Ramon Goñi, Alexandra Balaceanu, Guillem Portella, Federica Battistini, Josep Lluis Gelpí & Modesto Orozco

  3. School of Physics and Astronomy, University of Leeds, Leeds, UK

    Agnes Noy & Sarah A Harris

  4. Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA

    Alberto Pérez

  5. Barcelona Supercomputing Center, Barcelona, Spain

    Pau Andrio & Ramon Goñi

  6. Department of Chemistry, University of Cambridge, Cambridge, UK

    Guillem Portella & Michele Vendruscolo

  7. Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain

    Josep Lluis Gelpí & Modesto Orozco

  8. Instituto de Química Física 'Rocasolano', Consejo Superior de Investigaciones Cientificas, Madrid, Spain

    Carlos González

  9. School of Pharmacy, University of Nottingham, Nottingham, UK

    Charles A Laughton

  10. Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK

    Charles A Laughton

  11. Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA

    David A Case

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  1. Ivan Ivani
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Contributions

I.I. derived the parmbsc1 force-field parameter set. I.I., P.D.D., A.N., A.P., I.F., A.H., J.W., A.B., G.P., F.B., C.A.L. and S.A.H. performed validation simulations. C.G., M.V. and G.P. validated results from NMR-based experiments. C.G. obtained de novo NMR spectroscopy measurements. D.A.C. performed crystal MD simulations. R.G., P.A., A.H. and J.L.G. created the database infrastructure and web application. All authors contributed to data analysis. M.O. had the idea for the study, directed the project and wrote the manuscript, which was improved by the rest of the authors.

Corresponding author

Correspondence to Modesto Orozco.

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The authors declare no competing financial interests.

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Supplementary Figures 1–31, Supplementary Tables 1–12 and Supplementary Discussion (PDF 5701 kb)

Supplementary Software

Parmbsc1 parameters (ZIP 13 kb)

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Ivani, I., Dans, P., Noy, A. et al. Parmbsc1: a refined force field for DNA simulations. Nat Methods 13, 55–58 (2016). https://doi.org/10.1038/nmeth.3658

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