WeNMR: Structural Biology on the Grid

被引：151

作者：

Wassenaar, Tsjerk A. ^{[1
]}

van Dijk, Marc ^{[1
]}

Loureiro-Ferreira, Nuno ^{[1
]}

van der Schot, Gijs ^{[1
]}

de Vries, Sjoerd J. ^{[1
]}

Schmitz, Christophe ^{[1
]}

van der Zwan, Johan ^{[1
]}

Boelens, Rolf ^{[1
]}

Giachetti, Andrea ^{[2
]}

Ferella, Lucio ^{[2
]}

Rosato, Antonio ^{[2
]}

Bertini, Ivano ^{[2
]}

Herrmann, Torsten ^{[3
]}

Jonker, Hendrik R. A. ^{[4
,5
]}

Bagaria, Anurag ^{[5
,6
]}

Jaravine, Victor ^{[5
,6
]}

Guntert, Peter ^{[5
,6
]}

Schwalbe, Harald ^{[4
,5
]}

Vranken, Wim F. ^{[7
]}

Doreleijers, Jurgen F. ^{[8
]}

Vriend, Gert ^{[9
]}

Vuister, Geerten W. ^{[10
]}

Franke, Daniel ^{[11
]}

Kikhney, Alexey ^{[11
]}

Svergun, Dmitri I. ^{[11
]}

Fogh, Rasmus H. ^{[12
]}

Ionides, John ^{[12
]}

Laue, Ernest D. ^{[12
]}

Spronk, Chris ^{[13
]}

Jurksa, Simonas ^{[13
]}

Verlato, Marco ^{[14
]}

Badoer, Simone ^{[14
]}

Dal Pra, Stefano ^{[14
]}

Mazzucato, Mirco ^{[14
]}

Frizziero, Eric ^{[14
]}

Bonvin, Alexandre M. J. J. ^{[1
]}

机构：

[1] Univ Utrecht, Fac Sci, Bijvoet Ctr Biomol Res, NL-3584 CH Utrecht, Netherlands

[2] Univ Florence, Magnet Resonance Ctr, I-50019 Sesto Fiorentino, Italy

[3] Univ Lyon, UCB Lyon 1, ENS Lyon, Ctr RMN Hauts Champs,Inst Sci Analyt,CNRS,URM 528, F-69100 Villeurbanne, France

[4] Goethe Univ Frankfurt, Inst Organ Chem & Chem Biol, D-60438 Frankfurt, Germany

[5] Goethe Univ Frankfurt, Biomol Magnet Resonance Ctr, D-60438 Frankfurt, Germany

[6] Goethe Univ Frankfurt, Inst Biophys Chem, D-60438 Frankfurt, Germany

[7] European Bioinformat Inst, Cambridge CB10 1SD, England

[8] Radboud Univ Nijmegen, Prot Biophysics IMM, NL-6525 ED Nijmegen, Netherlands

[9] Radboud Univ Nijmegen, Med Ctr, CMBI, NL-6525 ED Nijmegen, Netherlands

[10] Univ Leicester, Sch Biol Sci, Dept Biochem, Leicester LE1 9HN, Leics, England

[11] European Mol Biol Lab, D-22603 Hamburg, Germany

[12] Univ Cambridge, Dept Biochem, Cambridge CB2 1GA, England

[13] UAB Spronk NMR Consultancy, LT-01402 Vilnius, Lithuania

[14] Ist Nazl Fis Nucl, Sez Padova, I-35131 Padua, Italy

来源：

JOURNAL OF GRID COMPUTING | 2012年 / 10卷 / 04期

基金：

英国生物技术与生命科学研究理事会;

关键词：

Web portals; Nuclear magnetic resonance; Small angle x-ray scattering; Structural biology; Proteins; Virtual research community; SMALL-ANGLE SCATTERING; MOLECULAR-STRUCTURE DETERMINATION; NMR STRUCTURE DETERMINATION; RAY SOLUTION SCATTERING; CHEMICAL-SHIFTS; FORCE-FIELD; TORSION ANGLE; STRUCTURE REFINEMENT; SEQUENCE HOMOLOGY; XPLOR-NIH;

D O I：

10.1007/s10723-012-9246-z

中图分类号：

TP [自动化技术、计算机技术];

学科分类号：

0812 ;

摘要：

The WeNMR (http://www.wenmr.eu) project is a European Union funded international effort to streamline and automate analysis of Nuclear Magnetic Resonance (NMR) and Small Angle X-Ray scattering (SAXS) imaging data for atomic and near-atomic resolution molecular structures. Conventional calculation of structure requires the use of various software packages, considerable user expertise and ample computational resources. To facilitate the use of NMR spectroscopy and SAXS in life sciences the WeNMR consortium has established standard computational workflows and services through easy-to-use web interfaces, while still retaining sufficient flexibility to handle more specific requests. Thus far, a number of programs often used in structural biology have been made available through application portals. The implementation of these services, in particular the distribution of calculations to a Grid computing infrastructure, involves a novel mechanism for submission and handling of jobs that is independent of the type of job being run. With over 450 registered users (September 2012), WeNMR is currently the largest Virtual Organization (VO) in life sciences. With its large and worldwide user community, WeNMR has become the first Virtual Research Community officially recognized by the European Grid Infrastructure (EGI).

引用

页码：743 / 767

页数：25

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