Publicaciones

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

  • Melero, Roberto
  • Sorzano, Carlos Oscar S.
  • Foster, Brent
  • Vilas, José Luis
  • Martínez, Marta
  • Marabini, Roberto
  • Ramiacute;rez-Aportela, Erney
  • Sanchez-Garcia, Ruben
  • Herreros, David
  • Del Caño, Laura
  • Losana, Patricia
  • Fonseca-Reyna, Yunior C.
  • Conesa, Pablo
  • Wrapp, Daniel
  • Chacon, Pablo
  • McLellan, Jason S.
  • Tagare, Hemant D.
  • Carazo, Jose Maria
Using a new consensus-based image-processing approach together with principal component analysis, the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state have been analysed. These studies revealed concerted motions involving the receptor-binding domain (RBD), N-terminal domain, and subdomains 1 and 2 around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. It is shown that in this data set there are not well defined, stable spike conformations, but virtually a continuum of states. An ensemble map was obtained with minimum bias, from which the extremes of the change along the direction of maximal variance were modeled by flexible fitting. The results provide a warning of the potential image-processing classification instability of these complicated data sets, which has a direct impact on the interpretability of the results., The authors would like to acknowledge financial support from
CSIC (PIE/COVID-19 No. 202020E079), the Comunidad de
Madrid through grant CAM (S2017/BMD-3817), the Spanish
Ministry of Science and Innovation through projects SEV
2017-0712, FPU-2015/264 and PID2019-104757RB-I00/AEI/
FEDER, the Instituto de Salud Carlos III [PT17/0009/0010
(ISCIII-SGEFI/ERDF)], and the European Union and
Horizon 2020 through grants INSTRUCT–ULTRA
(INFRADEV-03-2016-2017, Proposal 731005), EOSC Life
(INFRAEOSC-04-2018, Proposal 824087), HighResCells
(ERC-2018-SyG, Proposal 810057), IMpaCT (WIDESPREAD-
03-2018, Proposal 857203), CORBEL
(INFRADEV-1-2014-1, Proposal 654248) and EOSC–Synergy
(EINFRA-EOSC-5, Proposal 857647). HDT and BF were
supported by NIH grant GM125769 and JSM was supported
by NIH grant R01-AI127521



Technical Integration of Data Repositories: status and challenges

  • Bernal, Isabel
  • Tykhonov, Slava
  • Aguilar, Fernando
  • EOSC-SYNERGY
Presentation delivered in EOSC SYNERGY Second All Hands Meeting, Valencia, January 28-30, 2020., No



State of the art regarding digital badge issuing technologies

  • Moltó, Germán
  • Campos, Isabel
  • Hardt, Marcus
  • Blanquer, Ignacio
  • Caballer, Miguel
  • Orviz, Pablo
  • David, Mario
  • Gomes, Jorge
  • EOSC-SYNERGY
White paper document., This document analyses the existing services and tools that allow issuing digital badges with the purpose of selecting the most appropriate one to be adopted by EOSC-SYNERGY in order to issue proper recognition stamps to software that complies with the Software Quality Levels (SQA) metrics defined in the project., EOSC-SYNERGY receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 857647., Peer reviewed



EOSC Synergy WP6: Initial review of systems, initiatives and development of selection criteria of the online learning/training platforms and initiatives

  • Clare, Helen
  • Plóciennik, Marcin
  • Krzyżanek, Mateusz
  • Akwarski, Jacek
  • Bernal, Isabel
  • Cepinskas, Linas
  • Hof, Cees
  • Ruiz Manzanares, Gonzalo
  • Thomson, Chris
  • EOSC-SYNERGY
This report describes a review of possible learning platforms and tools, and relevant previous and current projects and initiatives in the area of Open Science and EOSC training and education. It also includes reflections on the criteria we will use to select the platform and tools for the EOSC-Synergy project., European Commission. The report is a deliverable of EOSC-synergy project (INFRAEOSC-05(b)), Grant agreement ID: 857647., Peer reviewed



A Set of Common Service Quality Assurance Baseline Criteria for Research Projects

  • Orviz, Pablo
  • David, Mario
  • Gomes, Jorge
  • Pina, Joâo
  • Bernardo, Samuel
  • Campos, Isabel
  • Moltó, Germán
  • Caballer, Miguel
  • Tykhonov, Vyacheslav
  • EOSC-SYNERGY
Members of the EOSC-Synergy collaboration, 2019-2020., Update on February 2022, The purpose of this document is to dene a set of quality standards, procedures and best practices to conform a Service Quality Assurance plan to serve as a reference within the European research ecosystem related projects for the adequate development, deployment, operation and integration of services into production research infrastructures., European Union’s Horizon 2020 research and innovation programme under grant agreement number 857647., No



EOSC-synergy: Landscaping Country Report for Spain

  • Blanquer, Ignacio
  • Campos, Isabel
  • Cuesta Ruíz, María
  • Figueroa Rojas, Inmaculada
  • EOSC-SYNERGY
Licencia Creative Commons Attribution 4.0, This landscape analysis report aims to provide an overview of the policies, practices, roadmaps, and strategies around funding, procuring, providing, accessing and sharing of services and resources in the EOSC scope in Spain., Peer reviewed



Multitarget Virtual Screening for Drug Repurposing in COVID19

  • Sorzano, Carlos Óscar S.
  • Crisman, Enrique
  • Carazo, José M.
  • León, Rafael
Therapeutic or preventive research for coronavirus SARS-CoV2 is an
extremely active topic of research since its outbreak in January 2020. In
this paper we report the results from a virtual drug screening analysis
that, to the best of our knowledge, is the widest work in terms of target
proteins and compound library. Our study was focused on the repur-
posing of currently commercialized drugs, and especially those that can
interact with multiple viral proteins and several binding sites within each
protein. Additionally, we performed a second virtual screening analysis in
which we compared our results to the predicted binding a nities for the
drugs currently in clinical trials. We show that the best molecules in our
screening compares favourably to those in clinical trials, suggesting their
suitability for therapeutic or preventive applications.Therapeutic or preventive research for coronavirus SARS-CoV2 is an
extremely active topic of research since its outbreak in January 2020. In
this paper we report the results from a virtual drug screening analysis
that, to the best of our knowledge, is the widest work in terms of target
proteins and compound library. Our study was focused on the repur-
posing of currently commercialized drugs, and especially those that can
interact with multiple viral proteins and several binding sites within each
protein. Additionally, we performed a second virtual screening analysis in
which we compared our results to the predicted binding a nities for the
drugs currently in clinical trials. We show that the best molecules in our
screening compares favourably to those in clinical trials, suggesting their
suitability for therapeutic or preventive applications., We thank nancial support from the Spanish Ministry of Economy and Competitiveness
through Grants BIO2016-76400-R(AEI/FEDER, UE), the \Comunidad
Autonoma de Madrid" through Grant: S2017/BMD-3817, Instituto de
Salud Carlos III, PT17/0009/0010 (ISCIII-SGEFI/ERDF), European Union
(EU) and Horizon 2020 through grants: CORBEL (INFRADEV-1-2014-1, Proposal:
654248), INSTRUCT-ULTRA (INFRADEV-03-2016-2017, Proposal: 731005),
EOSC Life (INFRAEOSC-04-2018, Proposal: 824087), HighResCells (ERC-
2018-SyG, Proposal: 810057), IMpaCT (WIDESPREAD-03-2018 - Proposal:
857203), EOSC-Synergy (EINFRA-EOSC-5, Proposal: 857647), and iNEXTDiscovery
(Proposal: 871037). The authors acknowledge the support and the
use of resources of Instruct, a Landmark ESFRI project., No



EOSC-SYNERGY. EU DELIVERABLE: D1.1 Exploitation and Dissemination Plan

  • Campos, Isabel
  • Plociennik, Marcin
  • EOSC-SYNERGY
Description of the activities and procedures to be executed in order to maximise the impact of the project and to protect the results, establishing the roadmap for their future exploitation., EOSC-SYNERGY receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 857647., Peer reviewed



EOSC-SYNERGY. EU DELIVERABLE: D1.4 Quality Plan

  • Gomes, Jorge
  • Campos, Isabel
  • Blanquer, Ignacio
  • EOSC-SYNERGY
This document describes the measures and procedures established to guarantee a smooth project execution and the quality of the project results including risk management., EOSC-SYNERGY receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 857647., Peer reviewed



EOSC-SYNERGY. EU DELIVERABLE: D2.1 Roadmap for integration of national capacities into the EOSC and Policy Gap analysis

  • Hardt, Marcus
  • Pulapa, Agnieszka
  • Campos, Isabel
  • Plociennik, Marcin
  • Azevedo, Alberto
  • EOSC-SYNERGY
This deliverable summarises the considerations made and decisions taken to arrive at the initial
roadmap for the integration of national capacities. To provide thematic services with available infrastructure as early as possible, the majority of the resources will be integrated with high priority with the EGI Federated Cloud, while the more work intensive components will be integrated after the “low hanging fruit” have already been integrated. The current status of adoption of the AARC Policy Pack across the infrastructure was assessed with a questionnaire, results of which are provided. Room for improvement was identified and will be addressed with targeted online training on identified gaps. As a result of this deliverable, the majority of the infrastructure can be integrated with EOSC via the EGI Federated Cloud, while a smaller part of the capacities requires a case by case handling and adaptation / integration of software solutions into the operation of the participating infrastructure partners., EOSC-SYNERGY receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 857647., Peer reviewed