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Defining distance restraints in HADDOCK

Nature Protocols volume 13, page 1503 (2018)Cite this article

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To the Editor — In a recent issue of Nature Protocols, Orbán-Németh et al.1 present a protocol to predict structural models of proteins and their complexes from mass spectrometry (MS) cross-linking data. We read the protocol with interest, as it uses third-party software including the HADDOCK web portal2 (http://haddock.science.uu.nl/) that we developed and maintain. While we endorse and encourage the inclusion of our software in other protocols and pipelines, it is important that its usage be accurately and correctly described to avoid problems and incorrect results that we, as primary developers, will have to troubleshoot.

Distance restraints are implemented in HADDOCK to force groups of atoms to be at a specific distance from each other. As stated in our Nature Protocols paper describing the web server3, a distance restraint is defined using Crystallography and NMR system (CNS)4 syntax, by two atom selections followed by three numbers—the target distance (d0), a lower margin (d–) and an upper margin (d+). These three numbers are used to define a distance range, by subtracting and adding, respectively, the lower and upper margins to the target distance. Within this range, the potential energy of the restraint is zero. Further, this flexible syntax allows for the same distance range to be expressed differently, with practically no implications for the quality of the final models.

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Authors and Affiliations

  1. Computational Structural Biology, Utrecht University, Utrecht, The Netherlands

    Alexandre M. J. J. Bonvin

  2. Bioinformatics Unit, Izmir Biomedicine and Genome Center, Izmir, Turkey

    Ezgi Karaca

  3. Structural and Computational Biology Unit, EMBL-Heidelberg, Heidelberg, Germany

    Panagiotis L. Kastritis

  4. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA

    João P. G. L. M. Rodrigues

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  1. Alexandre M. J. J. Bonvin
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  2. Ezgi Karaca
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  3. Panagiotis L. Kastritis
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  4. João P. G. L. M. Rodrigues
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Bonvin, A.M.J.J., Karaca, E., Kastritis, P.L. et al. Defining distance restraints in HADDOCK. Nat Protoc 13, 1503 (2018). https://doi.org/10.1038/s41596-018-0017-6

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