World-wide E-infrastructure for structural biology

Leistungen

Report on prototypes constructed using Big Data approaches

See Task 7.3

Report on requirements by other RI

See WP3 Task 1

Report on Final project conference

See WP1 Task 3

Interim report on T2.1

See WP2 Task 1

Report on existing metadata standards, and proposals for new vocabularies

See Task 7.4

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.

Summary report of SB community engagement

See WP2 Task 3

Report on industrial user engagement

See WP2 Task 3

EM quality assurance workflow

See Task 7.2

Report on available VMs with associated documentation/use case for each of them

See Task 5.4

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).

Update of requirements by other RI

See WP3 Task 1

Quality analysis workflow for predicted complexes

See Task 7.2

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.

Report on the activities of the help desk

See Task 5.2

Report on Virtual folder

See Task 6.1

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.

Report on Assembly queries

See Task 6.4

Overview (baseline) of services and portals to be integrated into the new VRE

See Task 5.3

ProteinCCD with new analysis options

See Task 7.1

Report on access and usage statistics of the various services

Metrics

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

Draft sustainability work plan

See WP1 Task 5

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.

Interim report on T2.2

See WP2 Task 2

Periodic report 1

See WP1 Task 3

Report on the access and usage statistics

Metrics

D1.1 Report on Kick off meeting

See WP1 Task 1

Assessment of the life cycle of structural data and comparison with other scientific data

See WP3 Task 2

VRE-integrated PDBe search and query APIs

See WP6

Organisation of a round table or joint meeting involving ESFRIs

See WP3 Task 1

Update report on activities of the helpdesk

See Task 5.2

ProteinCCD with construct scoring and ranking

See Task 7.1

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.

Publication of a joint document on the usage of structural data in different biomedical RIs

See WP3 Task 1

Multi-core implementation of PDB_REDO server

See Task 7.1

Sustainability report

See WP1 Task 5

Report on Provenance

See Task 6.3

Project web pages

See WP1 Task 3

Project portal

See Task 5.1

Veröffentlichungen

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

Autoren: Segura, Joan; Sanchez-Garcia, Ruben; Martinez, Marta; Cuenca-Alba, Jesus; Tabas-Madrid, Daniel; Sorzano, C.O.S; Carazo, JM
Veröffentlicht in: Bioinformatics, Ausgabe 32, 2015, ISSN 1367-4803
Herausgeber: Oxford University Press
DOI: 10.5281/zenodo.1038019

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

Autoren: 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
Veröffentlicht in: Nucleic Acids Research, Ausgabe 45/20, 2017, Seite(n) 11989-12004, ISSN 0305-1048
Herausgeber: Oxford University Press
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

Autoren: Robert Dagil, Charlotte O'Shea, Anders Nykjær, Alexandre M. J. J. Bonvin, Birthe B. Kragelund
Veröffentlicht in: Journal of Biological Chemistry, Ausgabe 288/6, 2013, Seite(n) 4424-4435, ISSN 0021-9258
Herausgeber: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/jbc.M112.434159

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

Autoren: Linda Cerofolini, Sabrina Amar, Janelle L. Lauer, Tommaso Martelli, Marco Fragai, Claudio Luchinat, Gregg B. Fields
Veröffentlicht in: Scientific Reports, Ausgabe 6/1, 2016, ISSN 2045-2322
Herausgeber: Nature Publishing Group
DOI: 10.1038/srep29511

Atomic structural details of a protein grafted onto gold nanoparticles

Autoren: Stefano Giuntini, Linda Cerofolini, Enrico Ravera, Marco Fragai, Claudio Luchinat
Veröffentlicht in: Scientific Reports, Ausgabe 7/1, 2017, ISSN 2045-2322
Herausgeber: Nature Publishing Group
DOI: 10.1038/s41598-017-18109-z

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

Autoren: Mikael Trellet, Adrien S. J. Melquiond, Alexandre M. J. J. Bonvin
Veröffentlicht in: PLoS ONE, Ausgabe 8/3, 2013, Seite(n) e58769, ISSN 1932-6203
Herausgeber: Public Library of Science
DOI: 10.1371/journal.pone.0058769

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

Autoren: Joerg Schaarschmidt, Bohdan Monastyrskyy, Andriy Kryshtafovych, Alexandre M.J.J. Bonvin
Veröffentlicht in: Proteins: Structure, Function, and Bioinformatics, Ausgabe 86, 2018, Seite(n) 51-66, ISSN 0887-3585
Herausgeber: Wiley-Liss Inc
DOI: 10.1002/prot.25407

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

Autoren: Katherine A. Gentry, Elke Prade, Carlo Barnaba, Meng Zhang, Mukesh Mahajan, Sang-Choul Im, G. M. Anantharamaiah, Satoshi Nagao, Lucy Waskell, Ayyalusamy Ramamoorthy
Veröffentlicht in: Scientific Reports, Ausgabe 7/1, 2017, ISSN 2045-2322
Herausgeber: Nature Publishing Group
DOI: 10.1038/s41598-017-08130-7

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

Autoren: 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
Veröffentlicht in: Proteins: Structure, Function, and Bioinformatics, Ausgabe 85/3, 2017, Seite(n) 417-423, ISSN 0887-3585
Herausgeber: Wiley-Liss Inc
DOI: 10.1002/prot.25198

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

Autoren: 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
Veröffentlicht in: Nature Communications, Ausgabe 9/1, 2018, ISSN 2041-1723
Herausgeber: Nature Publishing Group
DOI: 10.1038/s41467-018-03182-3

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

Autoren: 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
Veröffentlicht in: Scientific Reports, Ausgabe 7/1, 2017, ISSN 2045-2322
Herausgeber: Nature Publishing Group
DOI: 10.1038/s41598-017-08321-2

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

Autoren: Valeria Putignano, Antonio Rosato, Lucia Banci, Claudia Andreini
Veröffentlicht in: Nucleic Acids Research, Ausgabe 46/D1, 2017, Seite(n) D459-D464, ISSN 0305-1048
Herausgeber: Oxford University Press
DOI: 10.1093/nar/gkx989

Distributed computing for macromolecular crystallography

Autoren: Evgeny Krissinel, Ville Uski, Andrey Lebedev, Martyn Winn, Charles Ballard
Veröffentlicht in: Acta Crystallographica Section D Structural Biology, Ausgabe 74/2, 2018, Seite(n) 143-151, ISSN 2059-7983
Herausgeber: IUCR
DOI: 10.1107/S2059798317014565

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

Autoren: Bart van Beusekom, Wouter G. Touw, Mahidhar Tatineni, Sandeep Somani, Gunaretnam Rajagopal, Jinquan Luo, Gary L. Gilliland, Anastassis Perrakis, Robbie P. Joosten
Veröffentlicht in: Protein Science, Ausgabe 27/3, 2018, Seite(n) 798-808, ISSN 0961-8368
Herausgeber: Cold Spring Harbor Laboratory Press
DOI: 10.1002/pro.3353

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

Autoren: 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
Veröffentlicht in: Nucleic Acids Research, Ausgabe 46/5, 2018, Seite(n) 2660-2677, ISSN 0305-1048
Herausgeber: Oxford University Press
DOI: 10.1093/nar/gky044

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

Autoren: 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
Veröffentlicht in: Journal of Computer-Aided Molecular Design, Ausgabe 32/1, 2018, Seite(n) 175-185, ISSN 0920-654X
Herausgeber: Kluwer Academic Publishers
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

Autoren: G.C.P. van Zundert, A.M.J.J. Bonvin
Veröffentlicht in: Journal of Structural Biology, Ausgabe 195/2, 2016, Seite(n) 252-258, ISSN 1047-8477
Herausgeber: Academic Press
DOI: 10.1016/j.jsb.2016.06.011

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

Autoren: Dimitrios Spiliotopoulos, Panagiotis L. Kastritis, Adrien S. J. Melquiond, Alexandre M. J. J. Bonvin, Giovanna Musco, Walter Rocchia, Andrea Spitaleri
Veröffentlicht in: Frontiers in Molecular Biosciences, Ausgabe 3, 2016, ISSN 2296-889X
Herausgeber: Frontiers
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

Autoren: 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
Veröffentlicht in: Journal of Structural Biology, Ausgabe 200/1, 2017, Seite(n) 20-27, ISSN 1047-8477
Herausgeber: Academic Press
DOI: 10.1016/j.jsb.2017.06.004

Homology-based loop modeling yields more complete crystallographic protein structures

Autoren: Bart van Beusekom, Krista Joosten, Maarten L. Hekkelman, Robbie P. Joosten, Anastassis Perrakis
Veröffentlicht in: IUCrJ, Ausgabe 5/5, 2018, Seite(n) 585-594, ISSN 2052-2525
Herausgeber: IUCR
DOI: 10.1107/S2052252518010552

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

Autoren: Davide Sala, Andrea Giachetti, Antonio Rosato
Veröffentlicht in: AIMS Biophysics, Ausgabe 5/1, 2018, Seite(n) 77-96, ISSN 2377-9098
Herausgeber: AIMS Press
DOI: 10.3934/biophy.2018.1.77

The Life Cycle of Structural Biology Data

Autoren: Chris Morris
Veröffentlicht in: Data Science Journal, Ausgabe 17, 2018, ISSN 1683-1470
Herausgeber: Committee on Data for Science and Technology (CODATA) International Council for Science (ICSU)
DOI: 10.5334/dsj-2018-026

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

Autoren: Linda Cerofolini, Tommaso Staderini, Stefano Giuntini, Enrico Ravera, Marco Fragai, Giacomo Parigi, Roberta Pierattelli, Claudio Luchinat
Veröffentlicht in: JBIC Journal of Biological Inorganic Chemistry, Ausgabe 23/1, 2018, Seite(n) 71-80, ISSN 0949-8257
Herausgeber: Springer Verlag
DOI: 10.1007/s00775-017-1511-y

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

Autoren: Azzurra Carlon, Enrico Ravera, Giacomo Parigi, Garib N. Murshudov, Claudio Luchinat
Veröffentlicht in: Journal of Biomolecular NMR, 2018, ISSN 0925-2738
Herausgeber: Kluwer Academic Publishers
DOI: 10.1007/s10858-018-0212-3

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

Autoren: 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
Veröffentlicht in: Database, Ausgabe 2018, 2018, ISSN 1758-0463
Herausgeber: Oxford University Press
DOI: 10.1093/database/bay002

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

Autoren: Mahta Mirzaei, Saeed Mirdamadi, Mohamad Reza Ehsani, Mahmoud Aminlari
Veröffentlicht in: Journal of Food and Drug Analysis, Ausgabe 26/2, 2018, Seite(n) 696-705, ISSN 1021-9498
Herausgeber: National Laboratories of Foods and Drugs
DOI: 10.1016/j.jfda.2017.07.008

Validation of Structures in the Protein Data Bank

Autoren: 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,
Veröffentlicht in: Structure, Ausgabe 25/12, 2017, Seite(n) 1916-1927, ISSN 0969-2126
Herausgeber: Cell Press
DOI: 10.1016/j.str.2017.10.009

The archiving and dissemination of biological structure data

Autoren: Helen M Berman, Stephen K Burley, Gerard J Kleywegt, John L Markley, Haruki Nakamura, Sameer Velankar
Veröffentlicht in: Current Opinion in Structural Biology, Ausgabe 40, 2016, Seite(n) 17-22, ISSN 0959-440X
Herausgeber: Elsevier BV
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

Autoren: Zorica Latinović, Adrijana Leonardi, Lidija Kovačič, Cho Koh, Jernej Šribar, Alenka Bakija, Divi Venkateswarlu, R. Kini, Igor Križaj
Veröffentlicht in: Thrombosis and Haemostasis, Ausgabe 118/10, 2018, Seite(n) 1713-1728, ISSN 0340-6245
Herausgeber: Schattauer
DOI: 10.1055/s-0038-1669785

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

Autoren: 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
Veröffentlicht in: Structure, Ausgabe 25/3, 2018, Seite(n) 536-545, ISSN 0969-2126
Herausgeber: Cell Press
DOI: 10.1016/j.str.2017.01.004

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

Autoren: Oleg Kovalevskiy, Robert A. Nicholls, Fei Long, Azzurra Carlon, Garib N. Murshudov
Veröffentlicht in: Acta Crystallographica Section D Structural Biology, Ausgabe 74/3, 2018, Seite(n) 215-227, ISSN 2059-7983
Herausgeber: IUCR
DOI: 10.1107/S2059798318000979

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

Autoren: Panagiotis I. Koukos, Li C. Xue, Alexandre M. J. J. Bonvin
Veröffentlicht in: Journal of Computer-Aided Molecular Design, 2018, ISSN 0920-654X
Herausgeber: Kluwer Academic Publishers
DOI: 10.1007/s10822-018-0148-4

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

Autoren: Ruben Sanchez-Garcia, Carlos Sorzano, Jose Carazo, Joan Segura
Veröffentlicht in: Molecules, Ausgabe 22/12, 2017, Seite(n) 2230, ISSN 1420-3049
Herausgeber: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules22122230

Protein Glycosylation through Sulfur Fluoride Exchange (SuFEx) Chemistry: The Key Role of a Fluorosulfate Thiolactoside

Autoren: Alberto Marra, Jiajia Dong, Tiancheng Ma, Stefano Giuntini, Elisa Crescenzo, Linda Cerofolini, Marco Martinucci, Claudio Luchinat, Marco Fragai, Cristina Nativi, Alessandro Dondoni
Veröffentlicht in: Chemistry - A European Journal, 2018, ISSN 0947-6539
Herausgeber: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201803912

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

Autoren: Alessia Lasorsa, Idir Malki, François-Xavier Cantrelle, Hamida Merzougui, Emmanuelle Boll, Jean-Charles Lambert, Isabelle Landrieu
Veröffentlicht in: Frontiers in Molecular Neuroscience, Ausgabe 11, 2018, ISSN 1662-5099
Herausgeber: Frontiers Research Foundation
DOI: 10.3389/fnmol.2018.00421

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

Autoren: Katarina Elez, Alexandre M. J. J. Bonvin, Anna Vangone
Veröffentlicht in: BMC Bioinformatics, Ausgabe 19/S15, 2018, ISSN 1471-2105
Herausgeber: BioMed Central
DOI: 10.1186/s12859-018-2414-9

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

Autoren: Elisabetta Argenzio, Jeffrey Klarenbeek, Katarzyna M. Kedziora, Leila Nahidiazar, Tadamoto Isogai, Anastassis Perrakis, Kees Jalink, Wouter H. Moolenaar, Metello Innocenti
Veröffentlicht in: Journal of Biological Chemistry, Ausgabe 293/50, 2018, Seite(n) 19161-19176, ISSN 0021-9258
Herausgeber: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/jbc.RA118.002779

Using Scipion for stream image processing at Cryo-EM facilities

Autoren: 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
Veröffentlicht in: Journal of Structural Biology, Ausgabe 204/3, 2018, Seite(n) 457-463, ISSN 1047-8477
Herausgeber: Academic Press
DOI: 10.1016/j.jsb.2018.10.001

Characterization of PEGylated Asparaginase: New Opportunities from NMR Analysis of Large PEGylated Therapeutics

Autoren: Linda Cerofolini, Stefano Giuntini, Azzurra Carlon, Enrico Ravera, Vito Calderone, Marco Fragai, Giacomo Parigi, Claudio Luchinat
Veröffentlicht in: Chemistry - A European Journal, 2019, ISSN 0947-6539
Herausgeber: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201804488

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

Autoren: Davide Sala, Andrea Giachetti, Claudio Luchinat, Antonio Rosato
Veröffentlicht in: Journal of Biomolecular NMR, Ausgabe 66/3, 2016, Seite(n) 175-185, ISSN 0925-2738
Herausgeber: Kluwer Academic Publishers
DOI: 10.1007/s10858-016-0065-6

Data publication with the structural biology data grid supports live analysis

Autoren: 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,
Veröffentlicht in: Nature Communications, Ausgabe 7, 2016, Seite(n) 10882, ISSN 2041-1723
Herausgeber: Nature Publishing Group
DOI: 10.1038/ncomms10882

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

Autoren: G.C.P. van Zundert, M. Trellet, J. Schaarschmidt, Z. Kurkcuoglu, M. David, M. Verlato, A. Rosato, A.M.J.J. Bonvin
Veröffentlicht in: Journal of Molecular Biology, Ausgabe 429/3, 2017, Seite(n) 399-407, ISSN 0022-2836
Herausgeber: Academic Press
DOI: 10.1016/j.jmb.2016.11.032

The Electron Microscopy eXchange (EMX) initiative

Autoren: Roberto Marabini, Steven J. Ludtke, Stephen C. Murray, Wah Chiu, Jose M. de la Rosa-Trevín, Ardan Patwardhan, J. Bernard Heymann, Jose M. Carazo
Veröffentlicht in: Journal of Structural Biology, Ausgabe 194/2, 2016, Seite(n) 156-163, ISSN 1047-8477
Herausgeber: Academic Press
DOI: 10.1016/j.jsb.2016.02.008

EGI federated platforms supporting accelerated computing

Autoren: Marco VERLATO, Paolo Andreetto, Jan Astalos, Miroslav Dobrucky, Andrea Giachetti, David Rebatto, Antonio Rosato, Viet TRAN, Lisa Zangrando
Veröffentlicht in: Proceedings of International Symposium on Grids and Clouds (ISGC) 2017 — PoS(ISGC2017), 2017, Seite(n) 020
Herausgeber: Sissa Medialab
DOI: 10.22323/1.293.0020

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

Autoren: Irina de Sousa Moreira
Veröffentlicht in: Ausgabe 30, 2016
Herausgeber: University of Porto

Protein NMR

Autoren: Ranajeet Ghose
Veröffentlicht in: Methods in Molecular Biology, 2018, Seite(n) 111-132, ISBN 978-1-4939-7386-6
Herausgeber: Springer New York
DOI: 10.1007/978-1-4939-7386-6

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