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World-wide E-infrastructure for structural biology

Deliverables

Overview of external datasets, strategy of access methods, and implications on the portal architecture

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.

Report on the progress of the deployment of consolidated platform and its inteactions with infrastructure

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).

A HADDOCK server for EM

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.

Final report on deployment of consolidated platform and the overall architecture

This is a concluding deliverable of WP4, wrapping up all the WP work in the project.

Repositories

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.

Common security model design

See Task 4.4 The deliverable describes an overall design of the security model used in the services project-wide.

Consolidated architecture of job submission and interaction with infrastructure

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.

Final report

See WP1 Task 4

A REFMAC server for EM and NMR

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.

Periodic report 1

See WP1 Task 3

Report on experience with deployment of consolidated platform and its interaction with infrastructure

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.

Sustainability report

See WP1 Task 5

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Publications

3DBIONOTES v2.0: a web server for the automatic annotation of macromolecular structures

Author(s): Segura, Joan; Sanchez-Garcia, Ruben; Martinez, Marta; Cuenca-Alba, Jesus; Tabas-Madrid, Daniel; Sorzano, C.O.S; Carazo, JM
Published in: Bioinformatics, Issue 32, 2015, ISSN 1367-4803
DOI: 10.5281/zenodo.1038019

The basic tilted helix bundle domain of the prolyl isomerase FKBP25 is a novel double-stranded RNA binding module

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, Issue 45/20, 2017, Page(s) 11989-12004, ISSN 0305-1048
DOI: 10.1093/nar/gkx852

Gentamicin Binds to the Megalin Receptor as a Competitive Inhibitor Using the Common Ligand Binding Motif of Complement Type Repeats

Author(s): Robert Dagil, Charlotte O'Shea, Anders Nykjær, Alexandre M. J. J. Bonvin, Birthe B. Kragelund
Published in: Journal of Biological Chemistry, Issue 288/6, 2013, Page(s) 4424-4435, ISSN 0021-9258
DOI: 10.1074/jbc.M112.434159

Bilayer Membrane Modulation of Membrane Type 1 Matrix Metalloproteinase (MT1-MMP) Structure and Proteolytic Activity

Author(s): Linda Cerofolini, Sabrina Amar, Janelle L. Lauer, Tommaso Martelli, Marco Fragai, Claudio Luchinat, Gregg B. Fields
Published in: Scientific Reports, Issue 6/1, 2016, ISSN 2045-2322
DOI: 10.1038/srep29511

Atomic structural details of a protein grafted onto gold nanoparticles

Author(s): Stefano Giuntini, Linda Cerofolini, Enrico Ravera, Marco Fragai, Claudio Luchinat
Published in: Scientific Reports, Issue 7/1, 2017, ISSN 2045-2322
DOI: 10.1038/s41598-017-18109-z

A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking

Author(s): Mikael Trellet, Adrien S. J. Melquiond, Alexandre M. J. J. Bonvin
Published in: PLoS ONE, Issue 8/3, 2013, Page(s) e58769, ISSN 1932-6203
DOI: 10.1371/journal.pone.0058769

Assessment of contact predictions in CASP12: Co-evolution and deep learning coming of age

Author(s): Joerg Schaarschmidt, Bohdan Monastyrskyy, Andriy Kryshtafovych, Alexandre M.J.J. Bonvin
Published in: Proteins: Structure, Function, and Bioinformatics, Issue 86, 2018, Page(s) 51-66, ISSN 0887-3585
DOI: 10.1002/prot.25407

Kinetic and Structural Characterization of the Effects of Membrane on the Complex of Cytochrome b 5 and Cytochrome c

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, Issue 7/1, 2017, ISSN 2045-2322
DOI: 10.1038/s41598-017-08130-7

Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1

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, Issue 85/3, 2017, Page(s) 417-423, ISSN 0887-3585
DOI: 10.1002/prot.25198

A cryptic RNA-binding domain mediates Syncrip recognition and exosomal partitioning of miRNA targets

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, Issue 9/1, 2018, ISSN 2041-1723
DOI: 10.1038/s41467-018-03182-3

SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots

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, Issue 7/1, 2017, ISSN 2045-2322
DOI: 10.1038/s41598-017-08321-2

MetalPDB in 2018: a database of metal sites in biological macromolecular structures

Author(s): Valeria Putignano, Antonio Rosato, Lucia Banci, Claudia Andreini
Published in: Nucleic Acids Research, Issue 46/D1, 2017, Page(s) D459-D464, ISSN 0305-1048
DOI: 10.1093/nar/gkx989

Distributed computing for macromolecular crystallography

Author(s): Evgeny Krissinel, Ville Uski, Andrey Lebedev, Martyn Winn, Charles Ballard
Published in: Acta Crystallographica Section D Structural Biology, Issue 74/2, 2018, Page(s) 143-151, ISSN 2059-7983
DOI: 10.1107/S2059798317014565

Homology-based hydrogen bond information improves crystallographic structures in the PDB

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, Issue 27/3, 2018, Page(s) 798-808, ISSN 0961-8368
DOI: 10.1002/pro.3353

Sequence-specific DNA binding activity of the cross-brace zinc finger motif of the piggyBac transposase

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, Issue 46/5, 2018, Page(s) 2660-2677, ISSN 0305-1048
DOI: 10.1093/nar/gky044

Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2

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, Issue 32/1, 2018, Page(s) 175-185, ISSN 0920-654X
DOI: 10.1007/s10822-017-0049-y

Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-scale image pyramids

Author(s): G.C.P. van Zundert, A.M.J.J. Bonvin
Published in: Journal of Structural Biology, Issue 195/2, 2016, Page(s) 252-258, ISSN 1047-8477
DOI: 10.1016/j.jsb.2016.06.011

dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking

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, Issue 3, 2016, ISSN 2296-889X
DOI: 10.3389/fmolb.2016.00046

ScipionCloud: An integrative and interactive gateway for large scale cryo electron microscopy image processing on commercial and academic clouds

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, Issue 200/1, 2017, Page(s) 20-27, ISSN 1047-8477
DOI: 10.1016/j.jsb.2017.06.004

Homology-based loop modeling yields more complete crystallographic protein structures

Author(s): Bart van Beusekom, Krista Joosten, Maarten L. Hekkelman, Robbie P. Joosten, Anastassis Perrakis
Published in: IUCrJ, Issue 5/5, 2018, Page(s) 585-594, ISSN 2052-2525
DOI: 10.1107/S2052252518010552

Molecular dynamics simulations of metalloproteins: A folding study of rubredoxin from <em>Pyrococcus furiosus</em>

Author(s): Davide Sala, Andrea Giachetti, Antonio Rosato
Published in: AIMS Biophysics, Issue 5/1, 2018, Page(s) 77-96, ISSN 2377-9098
DOI: 10.3934/biophy.2018.1.77

The Life Cycle of Structural Biology Data

Author(s): Chris Morris
Published in: Data Science Journal, Issue 17, 2018, ISSN 1683-1470
DOI: 10.5334/dsj-2018-026

Long-range paramagnetic NMR data can provide a closer look on metal coordination in metalloproteins

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, Issue 23/1, 2018, Page(s) 71-80, ISSN 0949-8257
DOI: 10.1007/s00775-017-1511-y

Joint X-ray/NMR structure refinement of multidomain/multisubunit systems

Author(s): Azzurra Carlon, Enrico Ravera, Giacomo Parigi, Garib N. Murshudov, Claudio Luchinat
Published in: Journal of Biomolecular NMR, 2018, ISSN 0925-2738
DOI: 10.1007/s10858-018-0212-3

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

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, Issue 2018, 2018, ISSN 1758-0463
DOI: 10.1093/database/bay002

Production of antioxidant and ACE-inhibitory peptides from Kluyveromyces marxianus protein hydrolysates: Purification and molecular docking

Author(s): Mahta Mirzaei, Saeed Mirdamadi, Mohamad Reza Ehsani, Mahmoud Aminlari
Published in: Journal of Food and Drug Analysis, Issue 26/2, 2018, Page(s) 696-705, ISSN 1021-9498
DOI: 10.1016/j.jfda.2017.07.008

Validation of Structures in the Protein Data Bank

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, Issue 25/12, 2017, Page(s) 1916-1927, ISSN 0969-2126
DOI: 10.1016/j.str.2017.10.009

The archiving and dissemination of biological structure data

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, Issue 40, 2016, Page(s) 17-22, ISSN 0959-440X
DOI: 10.1016/j.sbi.2016.06.018

The First Intrinsic Tenase Complex Inhibitor with Serine Protease Structure Offers a New Perspective in Anticoagulant Therapy

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, Issue 118/10, 2018, Page(s) 1713-1728, ISSN 0340-6245
DOI: 10.1055/s-0038-1669785

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

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, Issue 25/3, 2018, Page(s) 536-545, ISSN 0969-2126
DOI: 10.1016/j.str.2017.01.004

Overview of refinement procedures within REFMAC 5: utilizing data from different sources

Author(s): Oleg Kovalevskiy, Robert A. Nicholls, Fei Long, Azzurra Carlon, Garib N. Murshudov
Published in: Acta Crystallographica Section D Structural Biology, Issue 74/3, 2018, Page(s) 215-227, ISSN 2059-7983
DOI: 10.1107/S2059798318000979

Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3

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
DOI: 10.1007/s10822-018-0148-4

3DCONS-DB: A Database of Position-Specific Scoring Matrices in Protein Structures

Author(s): Ruben Sanchez-Garcia, Carlos Sorzano, Jose Carazo, Joan Segura
Published in: Molecules, Issue 22/12, 2017, Page(s) 2230, ISSN 1420-3049
DOI: 10.3390/molecules22122230

Structural Basis of Tau Interaction With BIN1 and Regulation by Tau Phosphorylation

Author(s): Alessia Lasorsa, Idir Malki, François-Xavier Cantrelle, Hamida Merzougui, Emmanuelle Boll, Jean-Charles Lambert, Isabelle Landrieu
Published in: Frontiers in Molecular Neuroscience, Issue 11, 2018, ISSN 1662-5099
DOI: 10.3389/fnmol.2018.00421

Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classification

Author(s): Katarina Elez, Alexandre M. J. J. Bonvin, Anna Vangone
Published in: BMC Bioinformatics, Issue 19/S15, 2018, ISSN 1471-2105
DOI: 10.1186/s12859-018-2414-9

Profilin binding couples chloride intracellular channel protein CLIC4 to RhoA–mDia2 signaling and filopodium formation

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, Issue 293/50, 2018, Page(s) 19161-19176, ISSN 0021-9258
DOI: 10.1074/jbc.RA118.002779

Using Scipion for stream image processing at Cryo-EM facilities

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, Issue 204/3, 2018, Page(s) 457-463, ISSN 1047-8477
DOI: 10.1016/j.jsb.2018.10.001

A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions

Author(s): Davide Sala, Andrea Giachetti, Claudio Luchinat, Antonio Rosato
Published in: Journal of Biomolecular NMR, Issue 66/3, 2016, Page(s) 175-185, ISSN 0925-2738
DOI: 10.1007/s10858-016-0065-6

Data publication with the structural biology data grid supports live analysis

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, Issue 7, 2016, Page(s) 10882, ISSN 2041-1723
DOI: 10.1038/ncomms10882

The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes

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, Issue 429/3, 2017, Page(s) 399-407, ISSN 0022-2836
DOI: 10.1016/j.jmb.2016.11.032

The Electron Microscopy eXchange (EMX) initiative

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, Issue 194/2, 2016, Page(s) 156-163, ISSN 1047-8477
DOI: 10.1016/j.jsb.2016.02.008

EGI federated platforms supporting accelerated computing

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
DOI: 10.22323/1.293.0020

Supervised Classification Applied to Hot-Spot Detection in Protein-Protein Interfaces

Author(s): Irina de Sousa Moreira
Published in: Issue 30, 2016

Protein NMR

Author(s): Ranajeet Ghose
Published in: Methods in Molecular Biology, 2018, Page(s) 111-132
DOI: 10.1007/978-1-4939-7386-6