A worldwide e-Infrastructure for NMR and structural biology

WeNMR Partners

 

Bijvoet Center for Biomolecular Research

Utrecht University, The Netherlands

The Bijvoet Center for Biomolecular Research is a joint research institute of Utrecht University and the Chemical Sciences Research Council (NWO-CW) whose research focuses on mechanisms of molecular recognition and interactions. The research of the NMR group aims at obtaining fundamental insight in biological processes using the methods of high-resolution NMR spectroscopy. A major aim is to understand biomolecular recognition processes in terms of detailed 3D structures and dynamics. A further aim is the development of new methodology supporting the structural biology research. Novel methods have been and are being developed to make the structure determination process more efficient, to validate protein structures derived by NMR, to study dynamical processes of biomolecules, and to study transient states in photoreceptor molecules. The NMR group possesses a wide range of expertise in fields such as molecular biology, protein expression, development of new NMR methodology and its application to biomolecular systems, and development and application of computational and molecular modelling approaches. In the past, relaxation matrix-based structure refinement methods and validation software have been developed (IRMA, DINOSAUR, AQUA). A major achievement is the development of the protein-protein docking approach HADDOCK (High Ambiguity Driven protein-protein DOCKing) that can make use of biochemical and or biophysical information such as NMR titration data or mutagenesis data to drive the docking process. More than 700 research groups are now using this approach worldwide. The group has developed several user-friendly web portals for the structural biology community. The NMR group has and is participating to several EU-funded programs and networks contributing to the standardization of NMR computational approaches (FP5 RTD projects NMRQUAL and FIND, FP6 STREP projects Extend-NMR and NDDP) and is a core partner in the FP7 e-Infrastructure project e-NMR and in the Infrastructure projects EU-NMR and East-NMR. It also belongs to the large EU-funded Structural Genomics consortium SPINE-II complexes.

 

 

Center for Biomolecular Magnetic Resonance (BMRZ)

Johann Wolfgang Goethe University, Frankfurt am Main, Germany

The BMRZ currently has the largest number of NMR spectrometers of any EU NMR Infrastructure. Cryoprobe technology is available on all  instruments ranging from 600 MHz to 950 MHz. BMRZ is coordinating the I3 European network of NMR infrastructures (EU-NMR). BMRZ operates an internationally recognized Large Scale NMR Facility supporting biomolecular NMR research in the EU, being funded since 1995 under HCM, TMR and IHP. The research staff provide access, training and expertise to users who have determined many protein structures of ligand binding and catalytic domains including GPCRs, kinases and phosphatases. The institutes operate facilities for chemical synthesis, molecular biological and biochemical studies of the investigated systems. This site has developed a group of researchers entirely devoted to NMR in ligand design. Currently eight senior researchers are directly involved in related protein preparation, NMR screening and NMR structure. These researchers develop their own pulse programs, screening protocols and software and will focus on overcoming the technical problems of structural biological studies on membrane proteins.

 

 

Interuniversity Consortium for Magnetic Resonance on Metalloproteins (CIRMMP)

University of Florance, Italy

CIRMMP is the managing institution of the Magnetic Resonance Center of the University of Florence (CERM). CERM has a long-term, excellent knowledge and tradition in the characterization of structure and dynamics of proteins in solution through NMR. It has continuously contributed to the improvement of NMR- based techniques for macromolecular structure determination, and has been involved in European Structural Proteomics projects. It is equipped with the most advanced instruments for spectroscopic and biophysical characterization: 11 NMR nuclear magnetic resonance spectrometers, which span the largest range of existing magnetic fields, from very low (relaxometers) to very high ones (900 MHz). Most instruments are equipped with cryoprobes and several have optimized probes for paramagnetic systems, or automatic sample changers for large numbers of samples. Also the highest wide bore magnet spectrometer for solid state NMR (850 MHz) is available. The group also has access to EPR spectrometers and mass spectrometers (ESI- and MALDI-TOF), and apparatus for structural crystallography. Nearly 200 protein structures were solved in the laboratory using NMR and/or X-ray spectroscopies. The research group has considerable experience in structural biology, particularly in the characterisation through NMR of the structure and dynamics of proteins in solution as well as in the solid state; the group also has unique expertise in paramagnetic systems, having characterised several metalloproteins and developed software tools to include paramagnetism-based restraints in solution structure calculations. CIRMMP also has extensive experience in the development of new computational and experimental high- throughput screening methods and drug candidate optimisation, as well as in the application of the above- mentioned methodologies to selected disease targets. Finally, CIRMMP has a long-standing expertise in the application of bioinformatics to the analysis of genome sequences and of metalloproteins. CIRMMP is a core partner in the e-NMR e-Infrastructure project. CIRMMP has participated in several EC-funded projects. At present, CIRMMP is involved in the I3 projects EU- NMR and EAST-NMR as one of the research infrastructures providing transnational access to high-field instrumentation. CIRMMP is also involved in several RTD projects in Italy and in Europe, through STREPs. Finally, CIRMMP is a core lab of the INSTRUCT ESFRI infrastructure.

 

 

National Institute of Nuclear Physics    

Department of Physics Galileo Galilei, Padova, Itlay

INFN, is a public governmental research organization, which promotes, co- ordinates and funds nuclear and high-energy physics related researches. It is organized in 4 National Laboratories, 19 Departments (called Sections located in major Universities) and 11 Local Groups (see http://www.infn.it/mappa.php). INFN staff research personnel amounts to more than 1500 peoples with an equivalent number of associates from University and other Scientific National Institutes. INFN has a considerable experience on high performance distributed computing. Since 2001 INFN has played a major role in the EU DataGrid and DataTAG projects, the WLCG project, National Grid Projects GRID.IT and LIBI, and more recently the EGEE, EGEE-II and EGEE-III and the Grid infrastructure extension projects such as EUmedGRID, EUChinaGRID, EU-IndiaGrid1&2, EUAsiaGrid and EELA1&2, GridCC, OMII-EU, ETICS1&2 and OGF-EU. The contribution to these projects comprises the operation of the INFN Production GRID, with more than 10000 CPU’s deployed in 27 sites, the development and reengineering of many the Grid Middleware components already included in gLite (the Workload Management Service (WMS), the Virtual Organization Membership Service (VOMS), the Glue Schema, the CREAM-CE and CEmon, the Grid Accounting Service DGAS, the GRID Monitoring service GridICE), the ARGUS authorization framework and StoRM, an SRM interface to parallel file systems, together with dissemination ad training activities. Of particular relevance is also the role played by INFN in projects like LIBI, BioinfoGRID, e-NMR, CYCLOPS promoting the use of the grid technologies in other research communities. INFN is a core partner in the e-NMR e-infrastructure project that played a key role in deploying the e-NMR infrastructure.

 

 

Protein Biophysics, IMM and CMBI, NCMLS

Radboud University Nijmegen, The Netherlands

The groups of Profs Vuister/Vriend have worked for many years in close collaboration to develop methodology for improved structure generation and quality assessment of biomolecular structures. Their research clearly showed the need and the positive effects of proper refinement procedures in NMR-based structure determination. Their groups also develops software tools for these purposes; Vriend is the author of the well- known programs WHAT IF/WHAT CHECK and Vuister developed the program suite CING for the integrated, residue-based quality assessment of biomolecular structures and the program QUEEN, for the assessment of the NMR data. In addition, Vuister’s group employs high-resolution NMR spectroscopy and more recently also SAXS, to study proteins domains involved in the regulation of ion transport and the regulation and assembly of active biological complexes. For further biophysical characterization he also uses isothermal titration calorimetry and surface-plasmon resonance. The Vuister group is member of the Institute for Molecules and Materials (IMM) of the Radboud University Nijmegen, which also contains two other independent groups in the field of NMR (Profs Wijmenga and Kentgens).

Research of the Vriend group concerns the structural- and bioinformatics aspects of the biomolecular sciences. Using molecular- and homology modelling he studies proteins of biomedical interest. The group regularly examines de wwPDB and it associated data and undertakes large-scale recalculation efforts with the aim to test, improve and validate the most recent techniques. Examples of these efforts include the DRESS database of refined NMR structures and the recent PDB_REDO database of X-ray structures. The group also maintains a series of EBI-distributed databases, such as DSSP, HSSP, PDBFINDER and PDBREPORT. The Vriend group is member of the CMBI of the Nijmegen Center for Molecular life Sciences (NCMLS), a research centre of the Radboud University Medical Centre. The CMBI houses 3 other independent chairs in the bioinformatics field and hosts NBIC and the national Netherlands cheminformatics consortium.

 

 

University of Cambridge (UCAM)

Cambridge University, Cambridge, UK

Cambridge University is widely recognised as one of the world’s premier teaching and research universities. With around 400 research and support staff, the Biochemistry department is one of the largest departments in Cambridge, and undertakes internationally competitive research programs across a wide number of disciplines. Prof Laue’s group has a long track record in NMR method development, structural studies and Analytical NMR software development. For the last nine years the group has coordinated the Collaborative Computing Project in NMR (CCPN) which is involved in two major areas that overlap with the objectives of this application. CCPN has coordinated a program to define metadata standards for NMR, represented by the “CCPN data model”, and associated tools. By concentrating on developing representations of the intermediate states in the analysis of NMR data and tools for interconverting between the many different formats underlying software for analysing NMR data, CCPN has considerably eased the difficulty in exchanging data between programs. This is an essential prerequisite for developing pipeline software (such as the Extend-NMR GUI) and workflow managers important for WeNMR,

CCPN also has a strong track record in community development and outreach. Through a series of conferences, workshops and courses, CCPN has become the hub for the UK NMR community, and highly experienced in organising software outreach and community development. Typically, every year the group organises two conferences per year (one in the UK and one elsewhere in Europe), 5-10 courses and workshops (split between python programming and CcpNmr Analysis / Extend-NMR ) and 10-15 further talks, demonstrations, and working visits with collaborators across the UK, Europe, North America, and Australia. There is also an active Industry Group, which ensures that CCPN software meets the needs of users in pharmas and SMEs.

 

 

European Molecular Biology Laboratory (EMBL)

Hamburg Outstation, Hamburg, Germany

EMBL-Hamburg is an outstation of the European Molecular Biology Laboratory (EMBL) headquartered in Heidelberg. The Hamburg Outstation, a well-known centre for structural studies of biological macromolecules, is situated on the Deutsches Elektronen Synchrotron (DESY) site and has thirty years experience in the provision of synchrotron radiation in life sciences. The biological SAXS group at the EMBL- Hamburg runs a synchrotron small-angle scattering beamline X33 at the storage ring DORIS-3, dedicated to the studies of macromolecular solutions. The group is leading the efforts in the automation of the biological solution SAXS experiments. The X33 beamline has recently been completely refurbished and equipped with the world first robotic sample changer for SAXS, which successfully served already over 200 external user groups. The robot is linked to an automated data acquisition, processing and analysis pipeline for high throughput and remote SAXS studies. EMBL-Hamburg constructs a high brilliance BioSAXS beamline at the Petra-3 ring, to start operation in 2010, where the full automation will be implemented. The group also develops pioneering approaches for SAXS data analysis for biological macromolecules in solution. These novel developments, publicly available via the program package ATSAS are presently used in over 1000 laboratories and over 50% of biological SAXS publications worldwide are citing ATSAS programs. Most of these advanced analysis methods implement a multipronged approach, where SAXS is combined with other structural techniques, including crystallography, electron microscopy and NMR. The latter technique is especially actively used for rigid body analysis of multidomain and/or multisubunit macromolecules and complexes and also for the studies of flexible systems. The group established tight connections and fruitful collaborations with the leading biological solution NMR groups (including e.g. joint projects and publications with groups of A.Fersht, M.Sattler, M.Blackledge, I.Bertini, A.Pastore, M.Ubbink, M.Pons and others). EMBL Hamburg maintains a database DARA of over 10,000 SAXS patterns predicted from the PDB models, to rapidly search for the structural neighbours based on the experimental SAXS profiles. Recently, the SAXS group also opened access to the ATSAS-online service, where the modelling is performed over the Web interface. The online service has already over 350 users with over 7000 jobs run in the year 2009.

 

 

Spronk NMR Consultancy (SpronkNMR)

Vilnius, Lithuania

Spronk NMR Consultancy is a small enterprise that offers a variety of services and expertise in biomolecular NMR structure determination and validation to commercial and academic institutions worldwide. The company’s core specialisation lies in computational biomolecular NMR services, with the advantage that it combines high scientific standards with a practical hands-on approach. Therefore it is an ideal partner to test WeNMR technology in the development phase, address problems from the users’ perspective and develop training programs not only from a theoretical point of view but, more importantly, aimed at practical use of the WeNMR technology by non-experts. The knowledge present in the company spans the whole trajectory from biological experiments, NMR structure determination and refinement up to structure validation. In particular, the company has a unique expertise on the validation and the development of automated methods for the refinement of NMR structures of proteins (>10 publications with a total of >250 citations) that is not available in most research groups but is of critical importance and has a high added value for the results obtained from WeNMR applications. The current focus of the company is on developing and organizing courses on biomolecular NMR related topics, to make its knowledge widely available to the NMR community.

 

Academia Sinica (AS)



Taipei, Taiwan

Academia Sinica is the most preeminent academic institution in the Republic of China (Taiwan), which was founded in 1928 to promote and undertake scholarly research in sciences and humanities. Institute of Biological Chemistry (IBC) and Institute of Physics are two of the twenty-four research institutes and seven research centers, which are now headed by world-renowned scholars and staffed by highly trained, motivated, and creative young investigators. Starting from the year 2000, as to facing the new challenges in the post-genomics era, IBC has been devoted to the studies of Structural Biology and Functional Genomics. IBC continues to focus on Structural Biology and the main theme of "Proteins-from chemistry to biology". Academia Sinica houses the state-of-the-art National High-Field NMR Core Facility, consisting of six NMR spectrometers, ranging from 850MHz to 500 MHz, most of which are equipped with cryogenic probeheads. The facility is part of the Core Facilities for Protein Structural Analysis (CFPS) funded by the National Core Facility Program for Biotechnology (NCFPB) and the National Research Program for Biopharmaceuticals (NRPB). To broaden the horizons of Taiwan to the whole world, TWGrid has been established at the Institute of Physics with the mission of integration between national industries and Federal research application. Academia Sinica Grid Computing Center(ASGC) aims to establish a new way of national research infrastructure environment by sharing the experience earned in the collaboration with WLCG and e-Science project, developing various applications on eScience infrastructure in the collaboration with other technology fields, and utilizing technical support to provide a national research application environment of eScience infrastructure for fortify future national, Asia Pacific, and worldwide collaboration with the successful application for high energy physics and bioscience.

Cite WeNMR/WestLife

 
Usage of the WeNMR/WestLife portals should be acknowledged in any publication:
 
"The FP7 WeNMR (project# 261572) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid."
 
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

EGI-approved

The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858

West-Life