The West-Life project (https://about.west-life.eu/) is a Horizon 2020 project funded by the European Commission to provide data processing and data management services for the international community of structural biologists, and in particular to support integrative experimental approaches within the field of structural biology. It has developed enhancements to existing web services for structure solution and analysis, created new pipelines to link these services into more complex higher-level workflows, and added new data management facilities. Through this work it has striven to make the benefits of European e-Infrastructures more accessible to life-science researchers in general and structural biologists in particular.

Division of Biochemistry Netherlands Cancer Institute Amsterdam The Netherlands

European Molecular Biology Laboratory c o DESY Notkestr 85 22607 Hamburg Germany

European Molecular Biology Laboratory Cambridge UK

INFN Padova Division Italy

Instruct ERIC Oxford UK

Magnetic Resonance Center University of Florence Italy

Masaryk University Czech Republic

National Center for Biotechnology Spain

STFC Daresbury Laboratory Warrington UK

Utrecht University The Netherlands

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Hobor F., Dallmann A., Ball N.J., Cicchini C., Battistelli C., Ogrodowicz R.W., Christodoulou E., Martin S.R., Castello A., Tripodi M., Taylor I.A., Ramos A. A cryptic RNA-binding domain mediates syncrip recognition and exosomal partitioning of miRNA targets. Nat. Commun. 2018;9(1) doi: 10.1038/s41467-018-03182-3. PubMed DOI PMC

Ha B.H., Boggon T.J. The crystal structure of pseudokinase PEAK1 (sugen kinase 269) reveals an unusual catalytic cleft and a novel mode of kinase fold dimerization. J. Biol. Chem. 2017 doi: 10.1074/jbc.ra117.000751. jbc.RA117.000751+ PubMed DOI PMC

Long F., Vagin A.A., Young P., Murshudov G.N. IUCr, BALBES: a molecular-replacement pipeline. Acta Crystallogr. Sect. D: Biol. Crystallogr. 2008;64(1):125–132. doi: 10.1107/s0907444907050172. PubMed DOI PMC

Morris C. Towards a structural biology work bench. Acta Crystallogr. Sect. D. 2013;69(5):681–682. doi: 10.1107/s090744491300276x. PubMed DOI PMC

Winn M.D., Ballard C.C., Cowtan K.D., Dodson E.J., Emsley P., Evans P.R., Keegan R.M., Krissinel E.B., Leslie A.G.W., McCoy A., McNicholas S.J., Murshudov G.N., Pannu N.S., Potterton E.A., Powell H.R., Read R.J., Vagin A., Wilson K.S. IUCr, overview of the CCP4 suite and current developments. Acta Crystallogr. Sect. D: Biol. Crystallogr. 2011;67(4):235–242. doi: 10.1107/s0907444910045749. PubMed DOI PMC

Wassenaar T.A., van Dijk M., Loureiro-Ferreira N., van der Schot G., de Vries S.J., Schmitz C., van der Zwan J., Boelens R., Giachetti A., Ferella L., Rosato A., Bertini I., Herrmann T., Jonker H.R.A., Bagaria A., Jaravine V., Güntert P., Schwalbe H., Vranken W.F., Doreleijers J.F., Vriend G., Vuister G.W., Franke D., Kikhney A., Svergun D.I., Fogh R.H., Ionides J., Laue E.D., Spronk C., Jurkša S., Verlato M., Badoer S., Dal Pra S., Mazzucato M., Frizziero E., Bonvin A.M.J.J. WeNMR: structural biology on the grid. J. Grid Comput. 2012;10(4):743–767. doi: 10.1007/s10723-012-9246-z. DOI

Bertini I., Case D.A., Ferella L., Giachetti A., Rosato A. A grid-enabled web portal for NMR structure refinement with AMBER. Bioinformatics (Oxford, England) 2011;27(17):2384–2390. doi: 10.1093/bioinformatics/btr415. PubMed DOI

Verlato M., Andreetto P., Astalos J., Dobrucky M., Giachetti A., Rebatto D., Rosato A., Tran V., Zangrando L. Proceedings of International Symposium on Grids and Clouds (ISGC) 2017 – PoS(ISGC2017), Sissa Medialab. 2017. EGI federated platforms supporting accelerated computing. pp. 020+ DOI

Langer G., Cohen S.X., Lamzin V.S., Perrakis A. Automated macromolecular model building for x-ray crystallography using ARP/wARP version 7. Nat. Protoc. 2008;3(7):1171–1179. doi: 10.1038/nprot.2008.91. PubMed DOI PMC

van Zundert G.C.P., Trellet M., Schaarschmidt J., Kurkcuoglu Z., David M., Verlato M., Rosato A., Bonvin A.M.J.J. The DisVis and PowerFit web servers: explorative and integrative modeling of biomolecular complexes. J. Mol. Biol. 2017;429(3):399–407. doi: 10.1016/j.jmb.2016.11.032. PubMed DOI

Rinaldelli M., Ravera E., Calderone V., Parigi G., Murshudov G.N., Luchinat C. Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences. Acta Crystallogr. Sect. D. 2014;70(4):958–967. doi: 10.1107/s1399004713034160. PubMed DOI PMC

Vangone A., Rodrigues J.P., Xue L.C., van Zundert G.C., Geng C., Kurkcuoglu Z., Nellen M., Narasimhan S., Karaca E., van Dijk M., Melquiond A.S., Visscher K.M., Trellet M., Bonvin P.L., Kastritis A.M.J.J. Sense and simplicity in HADDOCK scoring: lessons from CASP-CAPRI round 1. Proteins: Struct. Funct. Bioinf. 2017;85(3):417–423. doi: 10.1002/prot.25198. PubMed DOI PMC

Spiliotopoulos D., Kastritis P.L., Melquiond A.S.J., Bonvin A.M.J.J., Musco G., Rocchia W., Spitaleri A. dMM-PBSA: a new HADDOCK scoring function for Protein-Peptide docking. Front. Mol. Biosci. 2016;3 doi: 10.3389/fmolb.2016.00046. PubMed DOI PMC

Putignano V., Rosato A., Banci L., Andreini C. MetalPDB in 2018: a database of metal sites in biological macromolecular structures. Nucleic Acids Res. 2018;46(D1) URL: http://view.ncbi.nlm.nih.gov/pubmed/29077942. PubMed PMC

Joosten R.P., Long F., Murshudov G.N., Perrakis A. The PDB_REDO server for macromolecular structure model optimization. IUCrJ. 2014;1(4):213–220. doi: 10.1107/s2052252514009324. PubMed DOI PMC

Mooij W.T.M., Mitsiki E., Perrakis A. ProteinCCD: enabling the design of protein truncation constructs for expression and crystallization experiments. Nucleic Acids Res. 37 (Web Server) 2009;W402–W405 doi: 10.1093/nar/gkp256. PubMed DOI PMC

Conesa Mingo P., Gutierrez J., Quintana A., de la Rosa Trevín J.M., Zaldívar-Peraza A., Cuenca Alba J., Kazemi M., Vargas J., del Cano L., Segura J., Sorzano C.O., Carazo J.M. Scipion web tools: easy to use cryo-EM image processing over the web. Protein Sci. 2017 doi: 10.1002/pro.3315. PubMed DOI PMC

Cuenca-Alba J., del Cano L., Gómez Blanco J., de la Rosa Trevín J.M., Conesa Mingo P., Marabini R., Sorzano C.O., Carazo J.M. ScipionCloud: an integrative and interactive gateway for large scale cryo electron microscopy image processing on commercial and academic clouds. J. Struct. Biol. 2017;200(1):20–27. doi: 10.1016/j.jsb.2017.06.004. PubMed DOI

Moreira I.S., Koukos P.I., Melo R., Almeida J.G., Preto A.J., Schaarschmidt J., Trellet M., Gümüş Z.H., Costa J., Bonvin A.M.J.J. SpotOn: high accuracy identification of protein-protein interface Hot-Spots. Scientific Rep. 2017;7(1) doi: 10.1038/s41598-017-08321-2. PubMed DOI PMC

Xue L.C., Rodrigues J.a.P.P., Kastritis P.L., Bonvin A.M.M., Vangone A. PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. Bioinformatics (Oxford England) 2016;32(23):3676–3678. doi: 10.1093/bioinformatics/btw514. PubMed DOI

Vangone A., Schaarschmidt J., Koukos P., Geng C., Citro N., Trellet M.E., Xue L.C., Bonvin A.M.J.J. Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server. Bioinformatics. 2018 doi: 10.1093/bioinformatics/bty816. PubMed DOI

Segura J., Sanchez-Garcia R., Martinez M., Cuenca-Alba J., Tabas-Madrid D., Sorzano C.O.S., Carazo J.M. 3DBIONOTES v2. 0: a web server for the automatic annotation of macromolecular structures. Bioinformatics. 2017;33(22):3655–3657. doi: 10.1093/bioinformatics/btx483. PubMed DOI PMC

Pereira J., Lamzin V.S. A distance geometry-based description and validation of protein main-chain conformation. IUCrJ. 2017;4(5):657–670. doi: 10.1107/s2052252517008466. PubMed DOI PMC

Lensink M.F., Velankar S., Wodak S.J. Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition. Proteins Struct. Function Bioinf. 2017;85(3):359–377. doi: 10.1002/prot.25215. PubMed DOI

van Zundert Bonvin. Fast and sensitive rigid-body fitting into cryo-EM density maps with PowerFit. AIMS Biophys. 2015;2(2):73–87. doi: 10.3934/biophy.2015.2.73. DOI

van Zundert G.C.P., Melquiond A.S.J., Bonvin A.M.J.J. Integrative modeling of biomolecular complexes: HADDOCKing with Cryo-Electron microscopy data. Structure. 2015;23(5):949–960. doi: 10.1016/j.str.2015.03.014. PubMed DOI

Berman H.M. The protein data bank. Nucleic Acids Res. 2000;28(1):235–242. doi: 10.1093/nar/28.1.235. PubMed DOI PMC

van Beusekom B., Touw W.G., Tatineni M., Somani S., Rajagopal G., Luo J., Gilliland G.L., Perrakis A., Joosten R.P. Homology-based hydrogen bond information improves crystallographic structures in the PDB. Protein Sci. 2018;27(3):798–808. doi: 10.1002/pro.3353. PubMed DOI PMC

Murshudov G.N., Skubák P., Lebedev A.A., Pannu N.S., Steiner R.A., Nicholls R.A., Winn M.D., Long F., Vagin A.A. IUCr, REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. Sect D: Biol. Crystallogr. 2011;67(4):355–367. doi: 10.1107/s0907444911001314. PubMed DOI PMC

Vangone A., Bonvin A.M.J.J. Contacts-based prediction of binding affinity in protein-protein complexes. eLife. 2015 URL: https://elifesciences.org/articles/07454. PubMed PMC

Wodak S.J., Janin J. Modeling protein assemblies: critical assessment of predicted interactions (CAPRI) 15 years hence. Proteins: Struct. Funct. Bioinf. 2017;85(3):357–358. doi: 10.1002/prot.25233. PubMed DOI

van Zundert G.C.P., Bonvin A.M.J.J. Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-scale image pyramids. J. Struct. Biol. 2016;195(2):252–258. doi: 10.1016/j.jsb.2016.06.011. PubMed DOI

Kurkcuoglu Z., Koukos P., Citro N., Trellet M., Rodrigues, Moreira I., Roel-Touris J., Melquiond A., Geng C., Schaarschmidt J., Xue L., Vangone A., Bonvin A.M.J.J. Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R grand challenge 2. J. Comput. Aided Mol. Des. 2018;32(1):175–185. doi: 10.1007/s10822-017-0049-y. PubMed DOI PMC

Keegan R.M., McNicholas S.J., Thomas J.M.H., Simpkin A.J., Simkovic F., Uski V., Ballard C.C., Winn M.D., Wilson K.S., Rigden D.J. IUCr, Recent developments in MrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment. Acta Crystallogr. Sect. D: Struct. Biol. 2018;74(3):167–182. doi: 10.1107/s2059798318003455. PubMed DOI PMC

Vagin A., Lebedev A. IUCr, MoRDa an automatic molecular replacement pipeline. Acta Crystallogr. Sect. A: Found. Adv. 2015;71 doi: 10.1107/s2053273315099672. DOI

Sehnal D., Deshpande M., Vařeková R.S., Mir S., Berka K., Midlik A., Pravda L., Velankar S., Koča J. LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data. Nat. Methods. 2017;14(12):1121–1122. doi: 10.1038/nmeth.4499. PubMed DOI

Salomoni D., Campos I., Gaido L., de Lucas J.M., Solagna P., Gomes J., Matyska L., Fuhrman P., Hardt M., Donvito G., Dutka L., Plociennik M., Barbera R., Blanquer I., Ceccanti A., Cetinic E., David M., Duma C., López-García A., Moltó G., Orviz P., Sustr Z., Viljoen M., Aguilar F., Alves L., Antonacci M., Antonelli L.A., Bagnasco S., Bonvin A.M.J.J., Bruno R., Chen Y., Costa A., Davidovic D., Ertl B., Fargetta M., Fiore S., Gallozzi S., Kurkcuoglu Z., Lloret L., Martins J., Nuzzo A., Nassisi P., Palazzo C., Pina J., Sciacca E., Spiga D., Tangaro M., Urbaniak M., Vallero S., Wegh B., Zaccolo V., Zambelli F., Zok T. INDIGO-DataCloud: a platform to facilitate seamless access to E-Infrastructures. J. Grid Comput. 2018;16(3):381–408. doi: 10.1007/s10723-018-9453-3. DOI

Crystallography: Protein data bank, 1971. Nat. New Biol. 233 (42), 223. https://doi.org/10.1038/newbio233223b0. DOI

Bernstein F.C., Koetzle T.F., Williams G.J.B., Meyer E.F., Brice M.D., Rodgers J.R., Kennard O., Shimanouchi T., Tasumi M. The protein data bank. A Computer-Based archival file for macromolecular structures. Eur. J. Biochem. 1977;80(2):319–324. doi: 10.1111/j.1432-1033.1977.tb11885.x. PubMed DOI

Wilkinson M.D., Dumontier M., Aalbersberg I.J., Appleton G., Axton M., Baak A., Blomberg N., Boiten J.-W., da Silva Santos L.B., Bourne P.E., Bouwman J., Brookes A.J., Clark T., Crosas M., Dillo I., Dumon O., Edmunds S., Evelo C.T., Finkers R., Gonzalez-Beltran A., Gray A.J.G., Groth P., Goble C., Grethe J.S., Heringa J., ’t Hoen P.A.C., Hooft R., Kuhn T., Kok R., Kok J., Lusher S.J., Martone M.E., Mons A., Packer A.L., Persson B., Rocca-Serra P., Roos M., van Schaik R., Sansone S.-A., Schultes E., Sengstag T., Slater T., Strawn G., Swertz M.A., Thompson M., van der Lei J., van Mulligen E., Velterop J., Waagmeester A., Wittenburg P., Wolstencroft K., Zhao J., Mons B. The FAIR guiding principles for scientific data management and stewardship. Scientific Data. 2016;3:160018+. doi: 10.1038/sdata.2016.18. PubMed DOI PMC