Acta Crystallographica Section D

Biological Crystallography

Volume 69, Part 5 (May 2013)

integrative structural biology

Acta Cryst. (2013). D69, 683-694    [ doi:10.1107/S0907444913007063 ]

On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys

E. Karaca and A. M. J. J. Bonvin

Abstract: Scoring, the process of selecting the biologically relevant solution from a pool of generated conformations, is one of the major challenges in the field of biomolecular docking. A prominent way to cope with this challenge is to incorporate information-based terms into the scoring function. Within this context, low-resolution shape data obtained from either ion-mobility mass spectrometry (IM-MS) or SAXS experiments have been integrated into the conventional scoring function of the information-driven docking program HADDOCK. Here, the strengths and weaknesses of IM-MS-based and SAXS-based scoring, either in isolation or in combination with the HADDOCK score, are systematically assessed. The results of an analysis of a large docking decoy set composed of dimers generated by running HADDOCK in ab initio mode reveal that the content of the IM-MS data is of too low resolution for selecting correct models, while scoring with SAXS data leads to a significant improvement in performance. However, the effectiveness of SAXS scoring depends on the shape and the arrangement of the complex, with prolate and oblate systems showing the best performance. It is observed that the highest accuracy is achieved when SAXS scoring is combined with the energy-based HADDOCK score.

Keywords: small-angle X-ray scattering; collision cross-section; ion-mobility mass spectrometry; HADDOCK; low resolution; hybrid methods.

pdfdisplay filedownload file

Portable Document Format (PDF) file (190.2 kbytes)
[ doi:10.1107/S0907444913007063/ic5089sup1.pdf ]
Supplementary material


To open or display or play some files, you may need to set your browser up to use the appropriate software. See the full list of file types for an explanation of the different file types and their related mime types and, where available links to sites from where the appropriate software may be obtained.

The download button will force most browsers to prompt for a file name to store the data on your hard disk.

Where possible, images are represented by thumbnails.

 bibliographic record in  format

  Find reference:   Volume   Page   
  Search:     From   to      Advanced search

Copyright © International Union of Crystallography
IUCr Webmaster