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Enabling proteins with RNA recognition motifs for synthetic biology and bio-analytics.

Deliverables

Online combined tool for screening RRMs for specific RNA binding

This software package will be made available via a web server, and will combine the features of all the previously developed software tools within the RNAct project via one single entry point.

Structure calculation software that better accounts for dynamics

This software tool will be linked to existing NMR structure calculation software, and will integrate information from experimental NMR data such as chemical shifts in order to ensure that the structure ensemble resulting from the structure calculation more accurately represents the dynamics of the molecule in solution.

RRM modelling & RNA-RRM docking software

A software package that will enable the modelling of RRMs from sequence, and the ability to dock RNAs to these models and to experimentally determined structures.

Tool for interpretation of RRMs in biophysical space

An integrated software tool will be created and made available that will link the sequence-based 'biophysical space' predictions from the Vranken group to RRM behaviour, such as RNA binding.

RNAct website and social media networks online

The RNAct website and social media channels are set up and working.

Online database for RRM sequences, conformations, and interactions

The database describing all the public and projectrelated information regarding RRM sequences conformations and interactions that can be made public at this point will be made available to the scientific community

Supervisory board

The Management and Supervisory board members, as well as subcommittee managers, are officially appointed and installed, with the first supervisory board meeting taken place. The supervisory board will consist of the following members: The network coordinator and the deputy coordinator: - Wim Vranken (network coordinator, VUB) - Michael Sattler (deputy coordinator, HMGU) The beneficiaries: - Isaure Chauvot de Beauchene (CNRS) - Guillermo Rodrigo (CSIC) - Karl Andersson (RV) - Tommaso Martelli (GIO) - Ulrich Rant (DBS) The partners: - André Matagne (ULg) - Malika Smail-Tabbone (UL) - Helena Danielson (UU) - Marco Fragai (UF) - Camelo Lópeza (UPV) - Martin Zacharias (TUM) - The to-be-appointed program manager - One of the RNAct ESRs (to be selected by their ESR peers) - Up to 3 external members (to be appointed)

Advertising of all ESR positions

All ESR positions will be advertised by the start of the project

Dedicated RNAct industry workshop for exploitation of results

A report describing the dedicated industry workshop where we explore the exploitation of the results Possible exploitation leads identified for beneficiaries in the project will only be included if they are considered for public use

All RNAct 7-monthly newsletters published

All RNAct newsletters every 7 months have been prepared and published in time

All annual agendas of outreach activities prepared and distributed

The outreach activity agendas for months 4 14 24 and 34 were prepared and distributed on time This deliverable is for all reports but will only be provided after the final outreach activity agenda See deliverable D64 for halfterm and final reports on their impact

Publications

Identification and Characterization of an RRM-Containing, RNA Binding Protein in Acinetobacter baumannii

Author(s): Caterina Ciani; Anna Pérez-Ràfols; Isabelle Bonomo; Mariachiara Micaelli; Alfonso Esposito; Chiara Zucal; Romina Belli; Vito Giuseppe D’Agostino; Irene Bianconi; Vito Calderone; Linda Cerofolini; Orietta Massidda; Michael Bernard Whalen; Marco Fragai; Alessandro Provenzani
Published in: Biomolecules, Issue 32, 2022, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom12070922

b2bTools: online predictions for protein biophysical features and their conservation

Author(s): Luciano Porto Kagami, Gabriele Orlando, Daniele Raimondi, Francois Ancien, Bhawna Dixit, Jose Gavaldá-García, Pathmanaban Ramasamy, Joel Roca-Martínez, Konstantina Tzavella, Wim Vranken
Published in: Nucleic Acids Research, Issue 31 May 2021, 2021, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab425

Gene regulation by a protein translation factor at the single-cell level

Author(s): Roswitha Dolcemascolo; Lucas Goiriz; Roser Montagud-Martínez; Guillermo Rodrigo
Published in: PLOS Computational BIology, Issue 10, 2022, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.5281/zenodo.7224967

Online biophysical predictions for SARS-CoV-2 proteins

Author(s): Luciano Kagami, Joel Roca-Martínez, Jose Gavaldá-García, Pathmanaban Ramasamy, K. Anton Feenstra, Wim F. Vranken
Published in: BMC Molecular and Cell Biology, Issue 22/1, 2021, ISSN 2661-8850
Publisher: BioMed Central Ltd.
DOI: 10.1186/s12860-021-00362-w

Deciphering the RRM-RNA recognition code: A computational analysis

Author(s): Roca-Martínez, Joel; Dhondge, Hrishikesh; Sattler, Michael; Vranken, Wim F.
Published in: PLOS Computational Biology, Issue 24, 2023, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1010859

Challenges in describing the conformation and dynamics of proteins with ambiguous behavior

Author(s): Roca-Martínez, Joel; Lazar, Tamas; Gavaldá-García, Jose; Bickel, David; Pancsa, Rita; Dixit, Bhawna; Tzavella, Konstantina; Ramasamy, Pathmanaban; Sanchez-Fornaris, Maite; Grau, Isel; Vranken, Wim
Published in: Frontiers in Molecular Biosciences, 2022, ISSN 2296-889X
Publisher: Frontiers Media S.A.
DOI: 10.3389/fmolb.2022.959956

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