Risultati finali
See Task 7.3
Report on requirements by other RISee WP3 Task 1
Report on Final project conferenceSee WP1 Task 3
Interim report on T2.1See WP2 Task 1
Report on existing metadata standards, and proposals for new vocabulariesSee Task 7.4
Overview of external datasets, strategy of access methods, and implications on the portal architectureSee Task 4.3 The deliverable is the initial output of the task (starting in year 2), giving the overview of datasets to be integrated to the project technical solutions.
Summary report of SB community engagementSee WP2 Task 3
Report on industrial user engagementSee WP2 Task 3
EM quality assurance workflowSee Task 7.2
Report on available VMs with associated documentation/use case for each of themSee Task 5.4
Report on the progress of the deployment of consolidated platform and its inteactions with infrastructureSee Task 4.1 This is an intermediate report on the consolidated architecture, based on full year experience with its deployment (after M4.1), updated with the experience with the second major deployment (M4.4).
Update of requirements by other RISee WP3 Task 1
Quality analysis workflow for predicted complexesSee Task 7.2
A HADDOCK server for EMWe have seen opportunities for improvements in the scientific approach that we planned. We have also decided to improve the sustainability of the service by moving to a more modern and secure software framework, Flask. Given the importance of both these objectives, we request a delay to M30.
Report on the activities of the help deskSee Task 5.2
Report on Virtual folderSee Task 6.1
Final report on deployment of consolidated platform and the overall architectureThis is a concluding deliverable of WP4, wrapping up all the WP work in the project.
RepositoriesWe have recognised that we will develop a more useful system if we allow more time for user experience studies, and therefore propose a delay in this deliverable.
Common security model designSee Task 4.4 The deliverable describes an overall design of the security model used in the services project-wide.
Report on Assembly queriesSee Task 6.4
Overview (baseline) of services and portals to be integrated into the new VRESee Task 5.3
ProteinCCD with new analysis optionsSee Task 7.1
Report on access and usage statistics of the various servicesMetrics
Consolidated architecture of job submission and interaction with infrastructureSee Task 4.2 The deliverable provides an overview of existing solution and a proposal for a consolidated architecture to be implemented in the project.
Final reportSee WP1 Task 4
Draft sustainability work planSee WP1 Task 5
A REFMAC server for EM and NMRA new opportunity was identified to integrate developments made by partner CIRRMP, which will enable joint structure solution using experimental data from NMR combined with data from X-ray experiments. Progress of this sort is central to West-Life's scientific goals, so it was decided to delay the deliverable in order to accomplish this work.
Interim report on T2.2See WP2 Task 2
Periodic report 1See WP1 Task 3
Report on the access and usage statisticsMetrics
D1.1 Report on Kick off meetingSee WP1 Task 1
Assessment of the life cycle of structural data and comparison with other scientific dataSee WP3 Task 2
VRE-integrated PDBe search and query APIsSee WP6
Organisation of a round table or joint meeting involving ESFRIsSee WP3 Task 1
Update report on activities of the helpdeskSee Task 5.2
ProteinCCD with construct scoring and rankingSee Task 7.1
Report on experience with deployment of consolidated platform and its interaction with infrastructureSee Task 4.1 The deliverable follows milestone M4.2, deployment of the new consolidated platform, and it reports on the initial experience with the deployment.
Publication of a joint document on the usage of structural data in different biomedical RIsSee WP3 Task 1
Multi-core implementation of PDB_REDO serverSee Task 7.1
Sustainability reportSee WP1 Task 5
See Task 6.3
Pubblicazioni
Autori:
Segura, Joan; Sanchez-Garcia, Ruben; Martinez, Marta; Cuenca-Alba, Jesus; Tabas-Madrid, Daniel; Sorzano, C.O.S; Carazo, JM
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Bioinformatics, Numero 32, 2015, ISSN 1367-4803
Editore:
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DOI:
10.5281/zenodo.1038019
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Nucleic Acids Research, Numero 45/20, 2017, Pagina/e 11989-12004, ISSN 0305-1048
Editore:
Oxford University Press
DOI:
10.1093/nar/gkx852
Autori:
Robert Dagil, Charlotte O'Shea, Anders Nykjær, Alexandre M. J. J. Bonvin, Birthe B. Kragelund
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Journal of Biological Chemistry, Numero 288/6, 2013, Pagina/e 4424-4435, ISSN 0021-9258
Editore:
American Society for Biochemistry and Molecular Biology Inc.
DOI:
10.1074/jbc.M112.434159
Autori:
Linda Cerofolini, Sabrina Amar, Janelle L. Lauer, Tommaso Martelli, Marco Fragai, Claudio Luchinat, Gregg B. Fields
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Scientific Reports, Numero 6/1, 2016, ISSN 2045-2322
Editore:
Nature Publishing Group
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10.1038/srep29511
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Stefano Giuntini, Linda Cerofolini, Enrico Ravera, Marco Fragai, Claudio Luchinat
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Scientific Reports, Numero 7/1, 2017, ISSN 2045-2322
Editore:
Nature Publishing Group
DOI:
10.1038/s41598-017-18109-z
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Mikael Trellet, Adrien S. J. Melquiond, Alexandre M. J. J. Bonvin
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PLoS ONE, Numero 8/3, 2013, Pagina/e e58769, ISSN 1932-6203
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Public Library of Science
DOI:
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Joerg Schaarschmidt, Bohdan Monastyrskyy, Andriy Kryshtafovych, Alexandre M.J.J. Bonvin
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Proteins: Structure, Function, and Bioinformatics, Numero 86, 2018, Pagina/e 51-66, ISSN 0887-3585
Editore:
Wiley-Liss Inc
DOI:
10.1002/prot.25407
Autori:
Katherine A. Gentry, Elke Prade, Carlo Barnaba, Meng Zhang, Mukesh Mahajan, Sang-Choul Im, G. M. Anantharamaiah, Satoshi Nagao, Lucy Waskell, Ayyalusamy Ramamoorthy
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Scientific Reports, Numero 7/1, 2017, ISSN 2045-2322
Editore:
Nature Publishing Group
DOI:
10.1038/s41598-017-08130-7
Autori:
A. Vangone, J. P. G. L. M. Rodrigues, L. C. Xue, G. C. P. van Zundert, C. Geng, Z. Kurkcuoglu, M. Nellen, S. Narasimhan, E. Karaca, M. van Dijk, A. S. J. Melquiond, K. M. Visscher, M. Trellet, P. L. Kastritis, A. M. J. J. Bonvin
Pubblicato in:
Proteins: Structure, Function, and Bioinformatics, Numero 85/3, 2017, Pagina/e 417-423, ISSN 0887-3585
Editore:
Wiley-Liss Inc
DOI:
10.1002/prot.25198
Autori:
Fruzsina Hobor, Andre Dallmann, Neil J. Ball, Carla Cicchini, Cecilia Battistelli, Roksana W. Ogrodowicz, Evangelos Christodoulou, Stephen R. Martin, Alfredo Castello, Marco Tripodi, Ian A. Taylor, Andres Ramos
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Nature Communications, Numero 9/1, 2018, ISSN 2041-1723
Editore:
Nature Publishing Group
DOI:
10.1038/s41467-018-03182-3
Autori:
Irina S. Moreira, Panagiotis I. Koukos, Rita Melo, Jose G. Almeida, Antonio J. Preto, Joerg Schaarschmidt, Mikael Trellet, Zeynep H. Gümüş, Joaquim Costa, Alexandre M. J. J. Bonvin
Pubblicato in:
Scientific Reports, Numero 7/1, 2017, ISSN 2045-2322
Editore:
Nature Publishing Group
DOI:
10.1038/s41598-017-08321-2
Autori:
Valeria Putignano, Antonio Rosato, Lucia Banci, Claudia Andreini
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Nucleic Acids Research, Numero 46/D1, 2017, Pagina/e D459-D464, ISSN 0305-1048
Editore:
Oxford University Press
DOI:
10.1093/nar/gkx989
Autori:
Evgeny Krissinel, Ville Uski, Andrey Lebedev, Martyn Winn, Charles Ballard
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Acta Crystallographica Section D Structural Biology, Numero 74/2, 2018, Pagina/e 143-151, ISSN 2059-7983
Editore:
IUCR
DOI:
10.1107/S2059798317014565
Autori:
Bart van Beusekom, Wouter G. Touw, Mahidhar Tatineni, Sandeep Somani, Gunaretnam Rajagopal, Jinquan Luo, Gary L. Gilliland, Anastassis Perrakis, Robbie P. Joosten
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Protein Science, Numero 27/3, 2018, Pagina/e 798-808, ISSN 0961-8368
Editore:
Cold Spring Harbor Laboratory Press
DOI:
10.1002/pro.3353
Autori:
Nelly Morellet, Xianghong Li, Silke A Wieninger, Jennifer L Taylor, Julien Bischerour, Séverine Moriau, Ewen Lescop, Benjamin Bardiaux, Nathalie Mathy, Nadine Assrir, Mireille Bétermier, Michael Nilges, Alison B Hickman, Fred Dyda, Nancy L Craig, Eric Guittet
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Nucleic Acids Research, Numero 46/5, 2018, Pagina/e 2660-2677, ISSN 0305-1048
Editore:
Oxford University Press
DOI:
10.1093/nar/gky044
Autori:
Zeynep Kurkcuoglu, Panagiotis I. Koukos, Nevia Citro, Mikael E. Trellet, J. P. G. L. M. Rodrigues, Irina S. Moreira, Jorge Roel-Touris, Adrien S. J. Melquiond, Cunliang Geng, Jörg Schaarschmidt, Li C. Xue, Anna Vangone, A. M. J. J. Bonvin
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Journal of Computer-Aided Molecular Design, Numero 32/1, 2018, Pagina/e 175-185, ISSN 0920-654X
Editore:
Kluwer Academic Publishers
DOI:
10.1007/s10822-017-0049-y
Autori:
G.C.P. van Zundert, A.M.J.J. Bonvin
Pubblicato in:
Journal of Structural Biology, Numero 195/2, 2016, Pagina/e 252-258, ISSN 1047-8477
Editore:
Academic Press
DOI:
10.1016/j.jsb.2016.06.011
Autori:
Dimitrios Spiliotopoulos, Panagiotis L. Kastritis, Adrien S. J. Melquiond, Alexandre M. J. J. Bonvin, Giovanna Musco, Walter Rocchia, Andrea Spitaleri
Pubblicato in:
Frontiers in Molecular Biosciences, Numero 3, 2016, ISSN 2296-889X
Editore:
Frontiers
DOI:
10.3389/fmolb.2016.00046
Autori:
Jesús Cuenca-Alba, Laura del Cano, Josué Gómez Blanco, José Miguel de la Rosa Trevín, Pablo Conesa Mingo, Roberto Marabini, Carlos Oscar S. Sorzano, Jose María Carazo
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Journal of Structural Biology, Numero 200/1, 2017, Pagina/e 20-27, ISSN 1047-8477
Editore:
Academic Press
DOI:
10.1016/j.jsb.2017.06.004
Autori:
Bart van Beusekom, Krista Joosten, Maarten L. Hekkelman, Robbie P. Joosten, Anastassis Perrakis
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IUCrJ, Numero 5/5, 2018, Pagina/e 585-594, ISSN 2052-2525
Editore:
IUCR
DOI:
10.1107/S2052252518010552
Autori:
Davide Sala, Andrea Giachetti, Antonio Rosato
Pubblicato in:
AIMS Biophysics, Numero 5/1, 2018, Pagina/e 77-96, ISSN 2377-9098
Editore:
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DOI:
10.3934/biophy.2018.1.77
Autori:
Chris Morris
Pubblicato in:
Data Science Journal, Numero 17, 2018, ISSN 1683-1470
Editore:
Committee on Data for Science and Technology (CODATA) International Council for Science (ICSU)
DOI:
10.5334/dsj-2018-026
Autori:
Linda Cerofolini, Tommaso Staderini, Stefano Giuntini, Enrico Ravera, Marco Fragai, Giacomo Parigi, Roberta Pierattelli, Claudio Luchinat
Pubblicato in:
JBIC Journal of Biological Inorganic Chemistry, Numero 23/1, 2018, Pagina/e 71-80, ISSN 0949-8257
Editore:
Springer Verlag
DOI:
10.1007/s00775-017-1511-y
Autori:
Azzurra Carlon, Enrico Ravera, Giacomo Parigi, Garib N. Murshudov, Claudio Luchinat
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Editore:
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Jasmine Y Young, John D Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M Berrisford, G Jawahar Swaminathan, Thomas J Oldfield, Aleksandras Gutmanas, Reiko Igarashi, David R Armstrong, Kumaran Baskaran, Li Chen, Minyu Chen, Alice R Clark, Luigi Di Costanzo, Dimitris Dimitropoulos, Guanghua Gao, Sutapa Ghosh, Swanand Gore, Vladimir Guranovic, Pieter M S Hendri
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Oxford University Press
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10.1093/database/bay002
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Mahta Mirzaei, Saeed Mirdamadi, Mohamad Reza Ehsani, Mahmoud Aminlari
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Cell Press
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10.22323/1.293.0020
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Irina de Sousa Moreira
Pubblicato in:
Numero 30, 2016
Editore:
University of Porto
Autori:
Ranajeet Ghose
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Editore:
Springer New York
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10.1007/978-1-4939-7386-6
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