Releasing the full potential of Instruct to expand and consolidate infrastructure services for integrated structural life science research

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Publications

Core Scientific Dataset Model: A lightweight and portable model and file format for multi-dimensional scientific data

Author(s): Deepansh J. Srivastava, Thomas Vosegaard, Dominique Massiot, Philip J. Grandinetti
Published in: PLOS ONE, 15/1, 2020, Page(s) e0225953, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0225953

Crystallographic binding studies of rat peroxisomal multifunctional enzyme type 1 with 3-ketodecanoyl-CoA: capturing active and inactive states of its hydratase and dehydrogenase catalytic sites

Author(s): Shruthi Sridhar, Werner Schmitz, J. Kalervo Hiltunen, Rajaram Venkatesan, Ulrich Bergmann, Tiila-Riikka Kiema, Rikkert K. Wierenga
Published in: Acta Crystallographica Section D Structural Biology, 76/12, 2020, Page(s) 1256-1269, ISSN 2059-7983
Publisher: International Union of Crystallography
DOI: 10.1107/s2059798320013819

Real-Time Quantitative In-Cell NMR: Ligand Binding and Protein Oxidation Monitored in Human Cells Using Multivariate Curve Resolution

Author(s): Enrico Luchinat, Letizia Barbieri, Timothy F. Campbell, Lucia Banci
Published in: Analytical Chemistry, 92/14, 2020, Page(s) 9997-10006, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.0c01677

Drug Screening in Human Cells by NMR Spectroscopy Allows the Early Assessment of Drug Potency

Author(s): Enrico Luchinat, Letizia Barbieri, Matteo Cremonini, Alessio Nocentini, Claudiu T. Supuran, Lucia Banci
Published in: Angewandte Chemie International Edition, 59/16, 2020, Page(s) 6535-6539, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201913436

Improvements on marker-free images alignment for electron tomography

Author(s): C.O.S. Sorzano, F. de Isidro-Gómez, E. Fernández-Giménez, D. Herreros, S. Marco, J.M. Carazo, C. Messaoudi
Published in: Journal of Structural Biology: X, 4, 2020, Page(s) 100037, ISSN 2590-1524
Publisher: Elsevier
DOI: 10.1016/j.yjsbx.2020.100037

Automatic local resolution-based sharpening of cryo-EM maps

Author(s): Erney Ramírez-Aportela, Jose Luis Vilas, Alisa Glukhova, Roberto Melero, Pablo Conesa, Marta Martínez, David Maluenda, Javier Mota, Amaya Jiménez, Javier Vargas, Roberto Marabini, Patrick M Sexton, Jose Maria Carazo, Carlos Oscar S Sorzano
Published in: Bioinformatics, 2019, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz671

Mechanistic Investigations of Green mEos4b Reveal a Dynamic Long-Lived Dark State

Author(s): Elke De Zitter, Jacqueline Ridard, Daniel Thédié, Virgile Adam, Bernard Lévy, Martin Byrdin, Guillaume Gotthard, Luc Van Meervelt, Peter Dedecker, Isabelle Demachy, Dominique Bourgeois
Published in: Journal of the American Chemical Society, 142/25, 2020, Page(s) 10978-10988, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.0c01880

Spectral editing of intra- and inter-chain methyl–methyl NOEs in protein complexes

Author(s): Ricarda Törner, Rida Awad, Pierre Gans, Bernhard Brutscher & Jerome Boisbouvier
Published in: Journal of Biomolecular NMR, 2020, ISSN 1573-5001
Publisher: Springer Nature
DOI: 10.1007/s10858-019-00293-x

MicrographCleaner: A python package for cryo-EM micrograph cleaning using deep learning

Author(s): Ruben Sanchez-Garcia, Joan Segura, David Maluenda, C.O.S. Sorzano, J.M. Carazo
Published in: Journal of Structural Biology, 210/3, 2020, Page(s) 107498, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2020.107498

Stabilizing the Closed SARS-CoV-2 Spike Trimer

Author(s): Jarek Juraszek, Lucy Rutten, Sven Blokland, Pascale Bouchier, Richard Voorzaat, Tina Ritschel, Mark J.G. Bakkers, Ludovic L.R. Renault, Johannes P.M. Langedijk
Published in: bioRxiv, 2020, ISSN 0000-0000
Publisher: bioRxiv
DOI: 10.1101/2020.07.10.197814

Cryo-EM structure of arabinosyltransferase EmbB from Mycobacterium smegmatis

Author(s): Yong Zi Tan, José Rodrigues, James E. Keener, Ruixiang Blake Zheng, Richard Brunton, Brian Kloss, Sabrina I. Giacometti, Ana L. Rosário, Lei Zhang, Michael Niederweis, Oliver B. Clarke, Todd L. Lowary, Michael T. Marty, Margarida Archer, Clinton S. Potter, Bridget Carragher, Filippo Mancia
Published in: Nature Communications, 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-17202-8

Mixing Aβ(1–40) and Aβ(1–42) peptides generates unique amyloid fibrils

Author(s): Linda Cerofolini, Enrico Ravera, Sara Bologna, Thomas Wiglenda, Annett Böddrich, Bettina Purfürst, Iryna Benilova, Magdalena Korsak, Gianluca Gallo, Domenico Rizzo, Leonardo Gonnelli, Marco Fragai, Bart De Strooper, Erich E. Wanker, Claudio Luchinat
Published in: Chemical Communications, 56/62, 2020, Page(s) 8830-8833, ISSN 1359-7345
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0cc02463e

Advanced isotopic labeling for the NMR investigation of challenging proteins and nucleic acids

Author(s): Jerome Boisbouvier, Lewis E. Kay
Published in: Journal of Biomolecular NMR, 71/3, 2018, Page(s) 115-117, ISSN 0925-2738
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10858-018-0199-9

Fast simulations of multidimensional NMR spectra of proteins and peptides

Author(s): Thomas Vosegaard
Published in: Magnetic Resonance in Chemistry, 56/6, 2018, Page(s) 438-448, ISSN 0749-1581
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/mrc.4663

Volta phase plate data collection facilitates image processing and cryo-EM structure determination

Author(s): Ottilie von Loeffelholz, Gabor Papai, Radostin Danev, Alexander G. Myasnikov, S. Kundhavai Natchiar, Isabelle Hazemann, Jean-François Ménétret, Bruno P. Klaholz
Published in: Journal of Structural Biology, 202/3, 2018, Page(s) 191-199, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2018.01.003

Visualization of chemical modifications in the human 80S ribosome structure

Author(s): S. Kundhavai Natchiar, Alexander G. Myasnikov, Hanna Kratzat, Isabelle Hazemann, Bruno P. Klaholz
Published in: Nature, 2017, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/nature24482

Function and Interactions of ERCC1-XPF in DNA Damage Response

Author(s): Maryam Faridounnia, Gert Folkers, Rolf Boelens
Published in: Molecules, 23/12, 2018, Page(s) 3205, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules23123205

Real-Time Insights into Biological Events: In-Cell Processes and Protein-Ligand Interactions

Author(s): Linda Cerofolini, Stefano Giuntini, Letizia Barbieri, Matteo Pennestri, Anna Codina, Marco Fragai, Lucia Banci, Enrico Luchinat, Enrico Ravera
Published in: Biophysical Journal, 116/2, 2019, Page(s) 239-247, ISSN 0006-3495
Publisher: Biophysical Society
DOI: 10.1016/j.bpj.2018.11.3132

Validation of electron microscopy initial models via small angle X-ray scattering curves

Author(s): Amaya Jiménez, Slavica Jonic, Tomas Majtner, Joaquín Otón, Jose Luis Vilas, David Maluenda, Javier Mota, Erney Ramírez-Aportela, Marta Martínez, Yaiza Rancel, Joan Segura, Ruben Sánchez-García, Roberto Melero, Laura del Cano, Pablo Conesa, Lars Skjaerven, Roberto Marabini, Jose M Carazo, Carlos Oscar S Sorzano
Published in: Bioinformatics, 35/14, 2018, Page(s) 2427-2433, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/bty985

Structures of influenza A virus RNA polymerase offer insight into viral genome replication

Author(s): Haitian Fan, Alexander P. Walker, Loïc Carrique, Jeremy R. Keown, Itziar Serna Martin, Dimple Karia, Jane Sharps, Narin Hengrung, Els Pardon, Jan Steyaert, Jonathan M. Grimes, Ervin Fodor
Published in: Nature, 573/7773, 2019, Page(s) 287-290, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-019-1530-7

CENP-A nucleosome clusters form rosette-like structures around HJURP during G1

Author(s): Leonid Andronov, Khalid Ouararhni, Isabelle Stoll, Bruno P. Klaholz, Ali Hamiche
Published in: Nature Communications, 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-12383-3

Deriving and refining atomic models in crystallography and cryo-EM: the latest Phenix tools to facilitate structure analysis

Author(s): Bruno P. Klaholz
Published in: Acta Crystallographica Section D Structural Biology, 75/10, 2019, Page(s) 878-881, ISSN 2059-7983
Publisher: IUCr/Wiley
DOI: 10.1107/s2059798319013391

Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion

Author(s): D. Maluenda, T. Majtner, P. Horvath, J. L. Vilas, A. Jiménez-Moreno, J. Mota, E. Ramírez-Aportela, R. Sánchez-García, P. Conesa, L. del Caño, Y. Rancel, Y. Fonseca, M. Martínez, G. Sharov, C.A. García, D. Strelak, R. Melero, R. Marabini, J. M. Carazo, C. O. S. Sorzano
Published in: Acta Crystallographica Section D Structural Biology, 75/10, 2019, Page(s) 882-894, ISSN 2059-7983
Publisher: IUCr/Wiley
DOI: 10.1107/s2059798319011860

DeepRes : a new deep-learning- and aspect-based local resolution method for electron-microscopy maps

Author(s): Erney Ramírez-Aportela, Javier Mota, Pablo Conesa, Jose Maria Carazo, Carlos Oscar S. Sorzano
Published in: IUCrJ, 6/6, 2019, Page(s) 1054-1063, ISSN 2052-2525
Publisher: IUCr
DOI: 10.1107/s2052252519011692

On the complementarity of X-ray and NMR data

Author(s): Antonio Schirò, Azzurra Carlon, Giacomo Parigi, Garib Murshudov, Vito Calderone, Enrico Ravera, Claudio Luchinat
Published in: Journal of Structural Biology: X, 4, 2020, Page(s) 100019, ISSN 2590-1524
Publisher: Elsevier
DOI: 10.1016/j.yjsbx.2020.100019

FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy

Author(s): David Střelák, Jiří Filipovič, Amaya Jiménez-Moreno, Jose Carazo, Carlos Sánchez Sorzano
Published in: Electronics, 9/6, 2020, Page(s) 1040, ISSN 2079-9292
Publisher: MDPI
DOI: 10.3390/electronics9061040

Towards a European health research and innovation cloud (HRIC)

Author(s): F. M. Aarestrup, A. Albeyatti, W. J. Armitage, C. Auffray, L. Augello, R. Balling, N. Benhabiles, G. Bertolini, J. G. Bjaalie, M. Black, N. Blomberg, P. Bogaert, M. Bubak, B. Claerhout, L. Clarke, B. De Meulder, G. D’Errico, A. Di Meglio, N. Forgo, C. Gans-Combe, A. E. Gray, I. Gut, A. Gyllenberg, G. Hemmrich-Stanisak, L. Hjorth, Y. Ioannidis, S. Jarmalaite, A. Kel, F. Kherif, J. O. Korbel, C. L
Published in: Genome Medicine, 12/1, 2020, ISSN 1756-994X
Publisher: BioMed Central
DOI: 10.1186/s13073-020-0713-z

Different flavors of diffusion in paramagnetic systems: Unexpected NMR signal intensity and relaxation enhancements

Author(s): Enrico Ravera, Marco Fragai, Giacomo Parigi, Claudio Luchinat
Published in: Journal of Magnetic Resonance Open, 2-3, 2020, Page(s) 100003, ISSN 2666-4410
Publisher: Elsevier
DOI: 10.1016/j.jmro.2020.100003

Solution of a Puzzle: High-Level Quantum-Chemical Treatment of Pseudocontact Chemical Shifts Confirms Classic Semiempirical Theory

Author(s): Lucas Lang, Enrico Ravera, Giacomo Parigi, Claudio Luchinat, Frank Neese
Published in: The Journal of Physical Chemistry Letters, 11/20, 2020, Page(s) 8735-8744, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.0c02462

Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures

Author(s): Roberto Melero, Carlos Oscar S. Sorzano, Brent Foster, José-Luis Vilas, Marta Martínez, Roberto Marabini, Erney Ramírez-Aportela, Ruben Sanchez-Garcia, David Herreros, Laura del Caño, Patricia Losana, Yunior C. Fonseca-Reyna, Pablo Conesa, Daniel Wrapp, Pablo Chacon, Jason S. McLellan, Hemant D. Tagare, Jose-Maria Carazo
Published in: IUCrJ, 7/6, 2020, Page(s) 1059-1069, ISSN 2052-2525
Publisher: International Union of Crystallography
DOI: 10.1107/s2052252520012725

Measurement of local resolution in electron tomography

Author(s): J.L. Vilas, J. Oton, C. Messaoudi, R. Melero, P. Conesa, E. Ramirez-Aportela, J. Mota, M. Martinez, A. Jimenez, R. Marabini, J.M. Carazo, J. Vargas, C.O.S. Sorzano
Published in: Journal of Structural Biology: X, 4, 2020, Page(s) 100016, ISSN 2590-1524
Publisher: Elsevier
DOI: 10.1016/j.yjsbx.2019.100016

Multitarget Virtual Screening for Drug Repurposing in COVID19

Author(s): carlos oscar Sorzano; Enrique Crisman; Jose Maria Carazo; rafael leon
Published in: Chemrxiv, 2, 2020, ISSN 2573-2293
Publisher: Chemrxiv
DOI: 10.26434/chemrxiv.12652997

A Topological Switch Enables Misfolding of the Cystic Fibrosis Transmembrane Conductance Regulator

Author(s): Daniel Scholl
Published in: bioRxiv, 2020, ISSN 0000-0000
Publisher: Biorxiv
DOI: 10.1101/2020.07.09.195099

FSC-Q: A CryoEM map-to-atomic model quality

Author(s): Ramírez-Aportela E, Maluenda D, Fonseca YC, Conesa P, Marabini R, Heymann JB, Carazo JM, Sorzano COS
Published in: BioRxiv, 2020, ISSN 2052-2525
Publisher: BioRxiv
DOI: 10.1101/2020.05.12.069831

Instruct-ULTRA D1.4 Dissemination, outreach and exploitation plan submitted to Executive Committee for review.

Author(s): Gray, Naomi; Owens, Ray
Published in: 1, 2017
Publisher: Zenodo
DOI: 10.5281/zenodo.4304625

Instruct-ULTRA D3.3 Process for establishing joint activities with new countries and formalising an agreement defining the shared programme

Author(s): Owens, Ray; Gray, Naomi
Published in: 8, 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4311654

Instruct-ULTRA D5.3 Information campaign addressing SMEs

Author(s): Chapman, Stephanie; Gray, Naomi; Morelli, Francesca; Owens, Ray
Published in: 1, 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4428101

Instruct-ULTRA D1.3 Women in Science Workshop

Author(s): Chrysina, Evangelia; Gray, Naomi; Chapman, Stephanie
Published in: 3, 2019
Publisher: Zenodo
DOI: 10.5281/zenodo.4304571

Instruct-ULTRA D2.4 Schedule of events to engage widely with key stakeholders

Author(s): Chapman, Stephanie; Gray, Naomi; Owens, Ray
Published in: 1, 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4304649

Instruct-ULTRA D7.2 Standardised workflows for integrative sample preparation methods for structural biology in cells

Author(s): Hart, Darren; Poterszman, Arnaud; van Ingen, Hugo; Boisbouvier, Jerome; Luchinat, Enrico
Published in: 5, 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4311800

Instruct-ULTRA D5.5 Outreach programme for new academic communities including an information pack

Author(s): Gray, Naomi; Owens, Ray
Published in: 1, 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4311775

Instruct-ULTRA D2.1 Plan a programme for review of Instruct Infrastructure with external review panel.

Author(s): Owens, Ray
Published in: 1, 2018
Publisher: Zenodo
DOI: 10.5281/zenodo.4304627

Instruct-ULTRA D6.2 VLE final version available to public

Author(s): Gray, Naomi; Chapman, Marysa; Perrakis, Anastassis
Published in: 2, 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4311781

Instruct-ULTRA D8.2 Process plan for raw and metadata archiving in subtask 8.1.2

Author(s): Smith, Neil; Carazo, Jose Maria
Published in: 12, 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4311808

Instruct-ULTRA D5.3 Information campaign addressing SMEs

Author(s): Chapman, Stephanie; Gray, Naomi; Owens, Ray
Published in: 9, 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4311758

Instruct-ULTRA D5.4 Long-Term Strategic Outreach Plan for both academic and industry users, including a training plan

Author(s): Owens, Ray; Daenke, Susan; Chapman, Stephanie; Gray, Naomi; Morelli, Francesca
Published in: 3, 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4317039

Instruct-ULTRA D1.2 Training programme for core facility and Instruct Centre staff

Author(s): Gray, Naomi; Chapman, Stephanie
Published in: 3, 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4304525

Instruct-ULTRA D8.1 Prototype process for data transfer defined in subtask 8.1.1

Author(s): Del Cano, Laura; White, Alex; Ashton, Alun; Smith, Neil; Carazo, Jose Maria
Published in: 3, 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4311804

Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM

Author(s): Tomasz Uchański, Simonas Masiulis, Baptiste Fischer, Valentina Kalichuk, Alexandre Wohlkönig, Thomas Zögg, Han Remaut, Wim Vranken, A. Radu Aricescu, Els Pardon, Jan Steyaert
Published in: bioRxiv, 2019
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/812230

MicrographCleaner: a python package for cryo-EM micrograph segmentation using deep learning.

Author(s): Sanchez-Garcia R, Segura J, Maluenda D, Sorzano CO, Carazo JM.
Published in: bioRxiv, 2019
Publisher: Cold Spring Harbor Laboratory

Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM.

Author(s): Uchanski T, Masiulis S, Fischer B, Kalichuk V, Wohlkonig A, Zogg T, Remaut H, Vranken W, Aricescu AR, Pardon E, Steyaert J.
Published in: bioRxiv, 2019
Publisher: Cold Spring Harbor Laboratory

Instruct-ULTRA D5.1 Public list of services offered to industries

Author(s): Banci, Lucia; Morelli, Francesca; Pierattelli, Roberta; Gray, Naomi
Published in: 7, 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4311748

Instruct-ULTRA D8.3 Develop enhanced deposition of structural data to database

Author(s): Conesa, Pablo
Published in: 11, 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4311810

Instruct-ULTRA D7.1 Standardised workflows for production, crystallisation and data collection of membrane proteins

Author(s): Archer, Magarida; Athayde, Diogo; van den Heuvel, Joop; Mohan Kaipa, Jagan; Krasnoselska, Ganna; Owens, Ray; Rodrigues, Jose; Rosario, Ana L.
Published in: 4, 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4311797

Instruct-ULTRA D4.1 Call 1 launched for developing new service provision of existing technologies and selection of qualifying projects

Author(s): Owens, Ray
Published in: 10, 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4311720

Instruct-ULTRA D6.3 Publication of a position paper on the operation of NMR services and RIs in general as a guide for users in collaboration with WP3

Author(s): Banci, Lucia; Boelens, Rolf; Morelli, Francesca; Pierattelli, Roberta; Wienk, Hans
Published in: 1, 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4311787

Instruct-ULTRA D6.5 Implemented software package for remote access EM data

Author(s): Bonnet, Frederic; Renault, Ludo
Published in: 6, 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4311793

In Vitro Production of Perdeuterated Proteins in H2O for Biomolecular NMR Studies

Author(s): Lionel Imbert, Rachel Lenoir-Capello, Elodie Crublet, Alicia Vallet, Rida Awad, Isabel Ayala, Celine Juillan-Binard, Hubert Mayerhofer, Rime Kerfah, Pierre Gans, Emeric Miclet, Jerome Boisbouvier
Published in: Structural Genomics - General Applications, 2199, 2021, Page(s) 127-149, ISBN 978-1-0716-0891-3
Publisher: Springer US
DOI: 10.1007/978-1-0716-0892-0_8

TFIIH: A multi-subunit complex at the cross-roads of transcription and DNA repair

Author(s): Olga Kolesnikova, Laura Radu, Arnaud Poterszman
Published in: DNA Repair, 115, 2019, Page(s) 21-67, ISBN 9780-128155592
Publisher: Elsevier
DOI: 10.1016/bs.apcsb.2019.01.003

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