Deliverables
See WP3 Task 1
See WP1 Task 3
See WP2 Task 1
See 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.
See WP2 Task 3
See WP2 Task 3
See Task 7.2
See 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).
See WP3 Task 1
See Task 7.2
We 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.
See Task 5.2
See Task 6.1
This is a concluding deliverable of WP4, wrapping up all the WP work in the project.
We 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.
See Task 4.4 The deliverable describes an overall design of the security model used in the services project-wide.
See Task 6.4
See Task 7.1
See Task 4.2 The deliverable provides an overview of existing solution and a proposal for a consolidated architecture to be implemented in the project.
See WP1 Task 4
See WP1 Task 5
A 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.
See WP2 Task 2
See WP1 Task 3
See WP1 Task 1
See WP3 Task 2
See Task 5.2
See Task 7.1
See 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.
See WP3 Task 1
See Task 7.1
See WP1 Task 5
See Task 6.3
See WP1 Task 3
See Task 5.1
Publications
Author(s): Segura, Joan; Sanchez-Garcia, Ruben; Martinez, Marta; Cuenca-Alba, Jesus; Tabas-Madrid, Daniel; Sorzano, C.O.S; Carazo, JM
Published in: Bioinformatics, 32, 2015, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.5281/zenodo.1038019
Author(s): David Dilworth, Santosh K. Upadhyay, Pierre Bonnafous, Amiirah Bibi Edoo, Sarah Bourbigot, Francy Pesek-Jardim, Geoff Gudavicius, Jason J. Serpa, Evgeniy V. Petrotchenko, Christoph H. Borchers, Christopher J. Nelson, Cameron D. Mackereth
Published in: Nucleic Acids Research, 45/20, 2017, Page(s) 11989-12004, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkx852
Author(s): Robert Dagil, Charlotte O'Shea, Anders Nykjær, Alexandre M. J. J. Bonvin, Birthe B. Kragelund
Published in: Journal of Biological Chemistry, 288/6, 2013, Page(s) 4424-4435, ISSN 0021-9258
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/jbc.M112.434159
Author(s): Linda Cerofolini, Sabrina Amar, Janelle L. Lauer, Tommaso Martelli, Marco Fragai, Claudio Luchinat, Gregg B. Fields
Published in: Scientific Reports, 6/1, 2016, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/srep29511
Author(s): Stefano Giuntini, Linda Cerofolini, Enrico Ravera, Marco Fragai, Claudio Luchinat
Published in: Scientific Reports, 7/1, 2017, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-017-18109-z
Author(s): Mikael Trellet, Adrien S. J. Melquiond, Alexandre M. J. J. Bonvin
Published in: PLoS ONE, 8/3, 2013, Page(s) e58769, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0058769
Author(s): Joerg Schaarschmidt, Bohdan Monastyrskyy, Andriy Kryshtafovych, Alexandre M.J.J. Bonvin
Published in: Proteins: Structure, Function, and Bioinformatics, 86, 2018, Page(s) 51-66, ISSN 0887-3585
Publisher: Wiley-Liss Inc
DOI: 10.1002/prot.25407
Author(s): Katherine A. Gentry, Elke Prade, Carlo Barnaba, Meng Zhang, Mukesh Mahajan, Sang-Choul Im, G. M. Anantharamaiah, Satoshi Nagao, Lucy Waskell, Ayyalusamy Ramamoorthy
Published in: Scientific Reports, 7/1, 2017, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-017-08130-7
Author(s): 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
Published in: Proteins: Structure, Function, and Bioinformatics, 85/3, 2017, Page(s) 417-423, ISSN 0887-3585
Publisher: Wiley-Liss Inc
DOI: 10.1002/prot.25198
Author(s): 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
Published in: Nature Communications, 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-03182-3
Author(s): 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
Published in: Scientific Reports, 7/1, 2017, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-017-08321-2
Author(s): Valeria Putignano, Antonio Rosato, Lucia Banci, Claudia Andreini
Published in: Nucleic Acids Research, 46/D1, 2017, Page(s) D459-D464, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkx989
Author(s): Evgeny Krissinel, Ville Uski, Andrey Lebedev, Martyn Winn, Charles Ballard
Published in: Acta Crystallographica Section D Structural Biology, 74/2, 2018, Page(s) 143-151, ISSN 2059-7983
Publisher: IUCR
DOI: 10.1107/S2059798317014565
Author(s): Bart van Beusekom, Wouter G. Touw, Mahidhar Tatineni, Sandeep Somani, Gunaretnam Rajagopal, Jinquan Luo, Gary L. Gilliland, Anastassis Perrakis, Robbie P. Joosten
Published in: Protein Science, 27/3, 2018, Page(s) 798-808, ISSN 0961-8368
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1002/pro.3353
Author(s): 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
Published in: Nucleic Acids Research, 46/5, 2018, Page(s) 2660-2677, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky044
Author(s): 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
Published in: Journal of Computer-Aided Molecular Design, 32/1, 2018, Page(s) 175-185, ISSN 0920-654X
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10822-017-0049-y
Author(s): G.C.P. van Zundert, A.M.J.J. Bonvin
Published in: Journal of Structural Biology, 195/2, 2016, Page(s) 252-258, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2016.06.011
Author(s): Dimitrios Spiliotopoulos, Panagiotis L. Kastritis, Adrien S. J. Melquiond, Alexandre M. J. J. Bonvin, Giovanna Musco, Walter Rocchia, Andrea Spitaleri
Published in: Frontiers in Molecular Biosciences, 3, 2016, ISSN 2296-889X
Publisher: Frontiers
DOI: 10.3389/fmolb.2016.00046
Author(s): 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
Published in: Journal of Structural Biology, 200/1, 2017, Page(s) 20-27, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2017.06.004
Author(s): Bart van Beusekom, Krista Joosten, Maarten L. Hekkelman, Robbie P. Joosten, Anastassis Perrakis
Published in: IUCrJ, 5/5, 2018, Page(s) 585-594, ISSN 2052-2525
Publisher: IUCR
DOI: 10.1107/S2052252518010552
Author(s): Davide Sala, Andrea Giachetti, Antonio Rosato
Published in: AIMS Biophysics, 5/1, 2018, Page(s) 77-96, ISSN 2377-9098
Publisher: AIMS Press
DOI: 10.3934/biophy.2018.1.77
Author(s): Chris Morris
Published in: Data Science Journal, 17, 2018, ISSN 1683-1470
Publisher: Committee on Data for Science and Technology (CODATA) International Council for Science (ICSU)
DOI: 10.5334/dsj-2018-026
Author(s): Linda Cerofolini, Tommaso Staderini, Stefano Giuntini, Enrico Ravera, Marco Fragai, Giacomo Parigi, Roberta Pierattelli, Claudio Luchinat
Published in: JBIC Journal of Biological Inorganic Chemistry, 23/1, 2018, Page(s) 71-80, ISSN 0949-8257
Publisher: Springer Verlag
DOI: 10.1007/s00775-017-1511-y
Author(s): Azzurra Carlon, Enrico Ravera, Giacomo Parigi, Garib N. Murshudov, Claudio Luchinat
Published in: Journal of Biomolecular NMR, 2018, ISSN 0925-2738
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10858-018-0212-3
Author(s): 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
Published in: Database, 2018, 2018, ISSN 1758-0463
Publisher: Oxford University Press
DOI: 10.1093/database/bay002
Author(s): Mahta Mirzaei, Saeed Mirdamadi, Mohamad Reza Ehsani, Mahmoud Aminlari
Published in: Journal of Food and Drug Analysis, 26/2, 2018, Page(s) 696-705, ISSN 1021-9498
Publisher: National Laboratories of Foods and Drugs
DOI: 10.1016/j.jfda.2017.07.008
Author(s): Swanand Gore, Eduardo Sanz García, Pieter M.S. Hendrickx, Aleksandras Gutmanas, John D. Westbrook, Huanwang Yang, Zukang Feng, Kumaran Baskaran, John M. Berrisford, Brian P. Hudson, Yasuyo Ikegawa, Naohiro Kobayashi, Catherine L. Lawson, Steve Mading, Lora Mak, Abhik Mukhopadhyay, Thomas J. Oldfield, Ardan Patwardhan, Ezra Peisach, Gaurav Sahni, Monica R. Sekharan, Sanchayita Sen, Chenghua Shao,
Published in: Structure, 25/12, 2017, Page(s) 1916-1927, ISSN 0969-2126
Publisher: Cell Press
DOI: 10.1016/j.str.2017.10.009
Author(s): Helen M Berman, Stephen K Burley, Gerard J Kleywegt, John L Markley, Haruki Nakamura, Sameer Velankar
Published in: Current Opinion in Structural Biology, 40, 2016, Page(s) 17-22, ISSN 0959-440X
Publisher: Elsevier BV
DOI: 10.1016/j.sbi.2016.06.018
Author(s): Zorica Latinović, Adrijana Leonardi, Lidija Kovačič, Cho Koh, Jernej Šribar, Alenka Bakija, Divi Venkateswarlu, R. Kini, Igor Križaj
Published in: Thrombosis and Haemostasis, 118/10, 2018, Page(s) 1713-1728, ISSN 0340-6245
Publisher: Schattauer
DOI: 10.1055/s-0038-1669785
Author(s): Jasmine Y. Young, John D. Westbrook, Zukang Feng, Raul Sala, Ezra Peisach, Thomas J. Oldfield, Sanchayita Sen, Aleksandras Gutmanas, David R. Armstrong, John M. Berrisford, Li Chen, Minyu Chen, Luigi Di Costanzo, Dimitris Dimitropoulos, Guanghua Gao, Sutapa Ghosh, Swanand Gore, Vladimir Guranovic, Pieter M.S. Hendrickx, Brian P. Hudson, Reiko Igarashi, Yasuyo Ikegawa, Naohiro Kobayashi, Catherine
Published in: Structure, 25/3, 2018, Page(s) 536-545, ISSN 0969-2126
Publisher: Cell Press
DOI: 10.1016/j.str.2017.01.004
Author(s): Oleg Kovalevskiy, Robert A. Nicholls, Fei Long, Azzurra Carlon, Garib N. Murshudov
Published in: Acta Crystallographica Section D Structural Biology, 74/3, 2018, Page(s) 215-227, ISSN 2059-7983
Publisher: IUCR
DOI: 10.1107/S2059798318000979
Author(s): Panagiotis I. Koukos, Li C. Xue, Alexandre M. J. J. Bonvin
Published in: Journal of Computer-Aided Molecular Design, 2018, ISSN 0920-654X
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10822-018-0148-4
Author(s): Ruben Sanchez-Garcia, Carlos Sorzano, Jose Carazo, Joan Segura
Published in: Molecules, 22/12, 2017, Page(s) 2230, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules22122230
Author(s): Alberto Marra, Jiajia Dong, Tiancheng Ma, Stefano Giuntini, Elisa Crescenzo, Linda Cerofolini, Marco Martinucci, Claudio Luchinat, Marco Fragai, Cristina Nativi, Alessandro Dondoni
Published in: Chemistry - A European Journal, 2018, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201803912
Author(s): Alessia Lasorsa, Idir Malki, François-Xavier Cantrelle, Hamida Merzougui, Emmanuelle Boll, Jean-Charles Lambert, Isabelle Landrieu
Published in: Frontiers in Molecular Neuroscience, 11, 2018, ISSN 1662-5099
Publisher: Frontiers Research Foundation
DOI: 10.3389/fnmol.2018.00421
Author(s): Katarina Elez, Alexandre M. J. J. Bonvin, Anna Vangone
Published in: BMC Bioinformatics, 19/S15, 2018, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-018-2414-9
Author(s): Elisabetta Argenzio, Jeffrey Klarenbeek, Katarzyna M. Kedziora, Leila Nahidiazar, Tadamoto Isogai, Anastassis Perrakis, Kees Jalink, Wouter H. Moolenaar, Metello Innocenti
Published in: Journal of Biological Chemistry, 293/50, 2018, Page(s) 19161-19176, ISSN 0021-9258
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/jbc.RA118.002779
Author(s): J. Gómez-Blanco, J.M. de la Rosa-Trevín, R. Marabini, L. del Cano, A. Jiménez, M. Martínez, R. Melero, T. Majtner, D. Maluenda, J. Mota, Y. Rancel, E Ramírez-Aportela, J.L. Vilas, M. Carroni, S. Fleischmann, E. Lindahl, A.W. Ashton, M. Basham, D.K. Clare, K. Savage, C.A. Siebert, G.G. Sharov, C.O.S. Sorzano, P. Conesa, J.M. Carazo
Published in: Journal of Structural Biology, 204/3, 2018, Page(s) 457-463, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2018.10.001
Author(s): Linda Cerofolini, Stefano Giuntini, Azzurra Carlon, Enrico Ravera, Vito Calderone, Marco Fragai, Giacomo Parigi, Claudio Luchinat
Published in: Chemistry - A European Journal, 2019, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201804488
Author(s): Davide Sala, Andrea Giachetti, Claudio Luchinat, Antonio Rosato
Published in: Journal of Biomolecular NMR, 66/3, 2016, Page(s) 175-185, ISSN 0925-2738
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10858-016-0065-6
Author(s): Peter A. Meyer, Stephanie Socias, Jason Key, Elizabeth Ransey, Emily C. Tjon, Alejandro Buschiazzo, Ming Lei, Chris Botka, James Withrow, David Neau, Kanagalaghatta Rajashankar, Karen S. Anderson, Richard H. Baxter, Stephen C. Blacklow, Titus J. Boggon, Alexandre M. J. J. Bonvin, Dominika Borek, Tom J. Brett, Amedeo Caflisch, Chung-I Chang, Walter J. Chazin, Kevin D. Corbett, Michael S. Cosgrove,
Published in: Nature Communications, 7, 2016, Page(s) 10882, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/ncomms10882
Author(s): G.C.P. van Zundert, M. Trellet, J. Schaarschmidt, Z. Kurkcuoglu, M. David, M. Verlato, A. Rosato, A.M.J.J. Bonvin
Published in: Journal of Molecular Biology, 429/3, 2017, Page(s) 399-407, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2016.11.032
Author(s): Roberto Marabini, Steven J. Ludtke, Stephen C. Murray, Wah Chiu, Jose M. de la Rosa-Trevín, Ardan Patwardhan, J. Bernard Heymann, Jose M. Carazo
Published in: Journal of Structural Biology, 194/2, 2016, Page(s) 156-163, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2016.02.008
Author(s): Marco VERLATO, Paolo Andreetto, Jan Astalos, Miroslav Dobrucky, Andrea Giachetti, David Rebatto, Antonio Rosato, Viet TRAN, Lisa Zangrando
Published in: Proceedings of International Symposium on Grids and Clouds (ISGC) 2017 — PoS(ISGC2017), 2017, Page(s) 020
Publisher: Sissa Medialab
DOI: 10.22323/1.293.0020
Author(s): Irina de Sousa Moreira
Published in: 30, 2016
Publisher: University of Porto
Author(s): Ranajeet Ghose
Published in: Methods in Molecular Biology, 2018, Page(s) 111-132, ISBN 978-1-4939-7386-6
Publisher: Springer New York
DOI: 10.1007/978-1-4939-7386-6
Datasets
Author(s): Bonvin, Alexandre MJJ.; Elez, Katarina; Vangone, Anna
Published in: SBGrid Data Bank
Author(s): Koukos, Panagiotis
Published in: SBGrid Data Bank
Author(s): Elez, Katarina; Bonvin, Alexandre; Vangone, Anna
Published in: figshare
Software
Author(s): van Zundert, Gydo; Bonvin, Alexandre
DOI: 10.5281/zenodo.1037227; 10.5281/zenodo.1037228
Publisher: Zenodo
Author(s): van Zundert, Gydo; Bonvin, Alexandre
DOI: 10.5281/zenodo.1037197; 10.5281/zenodo.1037196
Publisher: Zenodo