Journal of Biomolecular NMR

, Volume 53, Issue 4, pp 271–280 | Cite as

MaxOcc: a web portal for maximum occurrence analysis

  • Ivano Bertini
  • Lucio Ferella
  • Claudio Luchinat
  • Giacomo Parigi
  • Maxim V. Petoukhov
  • Enrico Ravera
  • Antonio Rosato
  • Dmitri I. Svergun
Article

Abstract

The MaxOcc web portal is presented for the characterization of the conformational heterogeneity of two-domain proteins, through the calculation of the Maximum Occurrence that each protein conformation can have in agreement with experimental data. Whatever the real ensemble of conformations sampled by a protein, the weight of any conformation cannot exceed the calculated corresponding Maximum Occurrence value. The present portal allows users to compute these values using any combination of restraints like pseudocontact shifts, paramagnetism-based residual dipolar couplings, paramagnetic relaxation enhancements and small angle X-ray scattering profiles, given the 3D structure of the two domains as input. MaxOcc is embedded within the NMR grid services of the WeNMR project and is available via the WeNMR gateway at http://py-enmr.cerm.unifi.it/access/index/maxocc. It can be used freely upon registration to the grid with a digital certificate.

Keywords

Paramagnetic NMR Conformational heterogeneity Ensemble averaging Grid computing Two-domain proteins 

Notes

Acknowledgments

We acknowledge funding by MIUR-FIRB contracts RBLA032ZM7, RBRN07BMCT, and by the European Commission, contracts Bio-NMR n. 261863, East-NMR n. 228461, Biomedbridges n. 284209 and We-NMR 261572. The WeNMR project is supported by the national GRID Initiatives of Belgium, Italy, Germany, the Netherlands (via the Dutch BiG Grid project), Portugal, the United Kingdom, South Africa, Taiwan and the Latin America GRID infrastructure via the Gisela project.

Supplementary material

10858_2012_9638_MOESM1_ESM.docx (263 kb)
Supplementary material 1 (DOCX 262 kb)

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Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Ivano Bertini
    • 1
    • 2
  • Lucio Ferella
    • 1
  • Claudio Luchinat
    • 1
    • 2
  • Giacomo Parigi
    • 1
    • 2
  • Maxim V. Petoukhov
    • 3
  • Enrico Ravera
    • 1
    • 2
  • Antonio Rosato
    • 1
    • 2
  • Dmitri I. Svergun
    • 3
  1. 1.Magnetic Resonance Center (CERM), University of FlorenceSesto FiorentinoItaly
  2. 2.Department of ChemistryUniversity of FlorenceSesto FiorentinoItaly
  3. 3.EMBL, Hamburg OutstationHamburgGermany

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