WeNMR

WeNMR is a worldwide e-Infrastructure for NMR spectroscopy and structural biology. It is the largest virtual Organization in the life sciences and is supported by EGI.

Goals

WeNMR aims at bringing together complementary research teams in the structural biology and life science area into a virtual research community at a worldwide level and provide them with a platform integrating and streamlining the computational approaches necessary for NMR and SAXS data analysis and structural modelling. Access to the infrastructure is provided through a portal integrating commonly used software and GRID technology.

Services

There are about 2 dozen computational NMR services available that can be divided into:

Processing: MDD NMR^[1]
Assignment: Auto Assign^[2] • MARS^[3] • UNIO^[4]
Analysis: TALOS+^[5] • AnisoFIT ^[6] • MaxOcc ^[7] • iCing
Structure Calculation: CS-ROSETTA • CYANA • UNIO^[4] • Xplor-NIH
Molecular Dynamics: AMBER • GROMACS
Modelling: 3D-DART ^[8] • HADDOCK^[9]
Tools: Format Converter ^[10] • SHIFTX2^[11] • Antechamber • PREDITOR^[12] • RCI^[13] • UPLABEL^[14]

Associated activities

Critical Assessment of Automated Structure Determination of Proteins from NMR Data (CASD-NMR ) is hosted by WeNMR.^[15] The first CASD-NMR paper, describing the results achieved in the 2009-2010 round, has been published in Structure.^[16]
The WeNMR facilitated the creation of an archive of 9000+ validation reports on Protein Data Bank structures in NRG-CING.^[17]
WeNMR closely collaborates with the ESFRI project Instruct for Integrated structural biology

History

The three-year WeNMR project started in November 2010 as the natural successor of the eNMR project. Financial support was provided by the European Community grants 213010 (eNMR) and 261572 (WeNMR) in the 7th Framework Programme (e-Infrastructure RI-261571).

Partners

Participant organisation name	Country
Universiteit Utrecht (BCBR) (Coordinator)	Netherlands
Johann Wolfgang Goethe Universitaet Frankfurt am Main (BMRZ)	Germany
Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP)	Italy
Istituto Nazionale di Fisica Nucleare (INFN)	Italy
Radboud Universiteit Nijmegen (RUN)	Netherlands
University of Cambridge (UCAM )	UK
European Molecular Biology Organization (EMBL) - Hamburg Outstation	Germany
Spronk NMR Consultancy SpronkNMR	Lithuania
Academia Sinica, Taipei	Taiwan

References

^ MDD NMR
^ Auto Assign
^ MARS
^ ^a ^b UNIO
^ TALOS+
^ Banci, L.; Bertini, I.; Huber, J. G.; Luchinat, C.; Rosato, A. (1998). "Partial Orientation of Oxidized and Reduced Cytochromeb5at High Magnetic Fields: Magnetic Susceptibility Anisotropy Contributions and Consequences for Protein Solution Structure Determination". Journal of the American Chemical Society. 120 (49): 12903. doi:10.1021/ja981791w.
^ Bertini, I.; Giachetti, A.; Luchinat, C.; Parigi, G.; Petoukhov, M. V.; Pierattelli, R.; Ravera, E.; Svergun, D. I. (2010). "Conformational Space of Flexible Biological Macromolecules from Average Data". Journal of the American Chemical Society. 132 (38): 13553–13558. doi:10.1021/ja1063923. PMID 20822180.
^ Van Dijk, M.; Bonvin, A. M. J. J. (2009). "3D-DART: A DNA structure modelling server". Nucleic Acids Research. 37 (Web Server issue): W235–W239. doi:10.1093/nar/gkp287. PMC 2703913. PMID 19417072.
^ HADDOCK
^ Vranken, W. F.; Boucher, W.; Stevens, T. J.; Fogh, R. H.; Pajon, A.; Llinas, M.; Ulrich, E. L.; Markley, J. L.; Ionides, J.; Laue, E. D. (2005). "The CCPN data model for NMR spectroscopy: Development of a software pipeline". Proteins: Structure, Function, and Bioinformatics. 59 (4): 687. doi:10.1002/prot.20449.
^ SHIFTX2
^ PREDITOR
^ RCI
^ UPLABEL
^ Rosato, A.; Aramini, J. M.; Arrowsmith, C.; Bagaria, A.; Baker, D.; Cavalli, A.; Doreleijers, J. F.; Eletsky, A.; Giachetti, A.; Guerry, P.; Gutmanas, A.; Güntert, P.; He, Y.; Herrmann, T.; Huang, Y. J.; Jaravine, V.; Jonker, H. R. A.; Kennedy, M. A.; Lange, O. F.; Liu, G.; Malliavin, T. R. S. E.; Mani, R.; Mao, B.; Montelione, G. T.; Nilges, M.; Rossi, P.; Van Der Schot, G.; Schwalbe, H.; Szyperski, T. A.; Vendruscolo, M. (2012). "Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data". Structure. 20 (2): 227–236. doi:10.1016/j.str.2012.01.002. PMC 3609704. PMID 22325772.
^ Rosato, A.; Bagaria, A.; Baker, D.; Bardiaux, B.; Cavalli, A.; Doreleijers, J. F.; Giachetti, A.; Guerry, P.; Güntert, P.; Herrmann, T.; Huang, Y. J.; Jonker, H. R. A.; Mao, B.; Malliavin, T. R. S. E.; Montelione, G. T.; Nilges, M.; Raman, S.; Van Der Schot, G.; Vranken, W. F.; Vuister, G. W.; Bonvin, A. M. J. J. (2009). "CASD-NMR: Critical assessment of automated structure determination by NMR". Nature Methods. 6 (9): 625–626. doi:10.1038/nmeth0909-625. PMC 2841015. PMID 19718014.
^ Doreleijers, J. F.; Vranken, W. F.; Schulte, C.; Markley, J. L.; Ulrich, E. L.; Vriend, G.; Vuister, G. W. (2011). "NRG-CING: Integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB". Nucleic Acids Research. 40 (Database issue): D519–D524. doi:10.1093/nar/gkr1134. PMC 3245154. PMID 22139937.

External links

The WeNMR VRC portal and website
WeNMR in the EU FP7 CORDIS database

[1] MDD NMR

[2] Auto Assign

[3] MARS

[Unio-4] UNIO

[5] TALOS+

[AnisoFIT-6] Banci, L.; Bertini, I.; Huber, J. G.; Luchinat, C.; Rosato, A. (1998). "Partial Orientation of Oxidized and Reduced Cytochromeb5at High Magnetic Fields: Magnetic Susceptibility Anisotropy Contributions and Consequences for Protein Solution Structure Determination". Journal of the American Chemical Society. 120 (49): 12903. doi:10.1021/ja981791w.

[MaxOcc-7] Bertini, I.; Giachetti, A.; Luchinat, C.; Parigi, G.; Petoukhov, M. V.; Pierattelli, R.; Ravera, E.; Svergun, D. I. (2010). "Conformational Space of Flexible Biological Macromolecules from Average Data". Journal of the American Chemical Society. 132 (38): 13553–13558. doi:10.1021/ja1063923. PMID 20822180.

[3D-DART-8] Van Dijk, M.; Bonvin, A. M. J. J. (2009). "3D-DART: A DNA structure modelling server". Nucleic Acids Research. 37 (Web Server issue): W235–W239. doi:10.1093/nar/gkp287. PMC 2703913. PMID 19417072.

[9] HADDOCK

[FormatConverter-10] Vranken, W. F.; Boucher, W.; Stevens, T. J.; Fogh, R. H.; Pajon, A.; Llinas, M.; Ulrich, E. L.; Markley, J. L.; Ionides, J.; Laue, E. D. (2005). "The CCPN data model for NMR spectroscopy: Development of a software pipeline". Proteins: Structure, Function, and Bioinformatics. 59 (4): 687. doi:10.1002/prot.20449.

[11] SHIFTX2

[12] PREDITOR

[13] RCI

[14] UPLABEL

[CASD-NMR2012-15] Rosato, A.; Aramini, J. M.; Arrowsmith, C.; Bagaria, A.; Baker, D.; Cavalli, A.; Doreleijers, J. F.; Eletsky, A.; Giachetti, A.; Guerry, P.; Gutmanas, A.; Güntert, P.; He, Y.; Herrmann, T.; Huang, Y. J.; Jaravine, V.; Jonker, H. R. A.; Kennedy, M. A.; Lange, O. F.; Liu, G.; Malliavin, T. R. S. E.; Mani, R.; Mao, B.; Montelione, G. T.; Nilges, M.; Rossi, P.; Van Der Schot, G.; Schwalbe, H.; Szyperski, T. A.; Vendruscolo, M. (2012). "Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data". Structure. 20 (2): 227–236. doi:10.1016/j.str.2012.01.002. PMC 3609704. PMID 22325772.

[CASD-NMR2009-16] Rosato, A.; Bagaria, A.; Baker, D.; Bardiaux, B.; Cavalli, A.; Doreleijers, J. F.; Giachetti, A.; Guerry, P.; Güntert, P.; Herrmann, T.; Huang, Y. J.; Jonker, H. R. A.; Mao, B.; Malliavin, T. R. S. E.; Montelione, G. T.; Nilges, M.; Raman, S.; Van Der Schot, G.; Vranken, W. F.; Vuister, G. W.; Bonvin, A. M. J. J. (2009). "CASD-NMR: Critical assessment of automated structure determination by NMR". Nature Methods. 6 (9): 625–626. doi:10.1038/nmeth0909-625. PMC 2841015. PMID 19718014.

[NRG-CING-17] Doreleijers, J. F.; Vranken, W. F.; Schulte, C.; Markley, J. L.; Ulrich, E. L.; Vriend, G.; Vuister, G. W. (2011). "NRG-CING: Integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB". Nucleic Acids Research. 40 (Database issue): D519–D524. doi:10.1093/nar/gkr1134. PMC 3245154. PMID 22139937.

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