BioExcel Centre of Excellence for Computational Biomolecular Research

Livrables

This document will include an updated training needs analysis and an outline of the BioExcel Training programme.

Initial deliverable stating the management organization and planning for the entire project.

The roadmap for each of the core applications will be updated for new changes to HPC hardware and software contexts, user requests, and progress since previous roadmaps, including strategies to balance user requests with developer-identified software needs.

Dissemination and outreach plan

This document will outline the overall plan for dissemination and outreach activities of the CoE.

State-of-the-art and Initial Roadmap

This deliverable will summarise and describe the new technologies, methods and tools identified and collected to be used in the project workflows. From these, an initial roadmap will be proposed.

Collaboration plan

In collaboration with CASTIEL-2 CSA and complementary projects, the plan will identify synergies and common objectives for collaboration with EuroHPC JU HPC Centers, CoEs and CC. It will outline the activities and define related project-specific milestones. The collaboration plan will be updated whenever significant changes arise and before every periodic assessment of the project.

Report on User Support Processes

Description of established procedures for overall BioExcel-3 user support, including move of all support to BioExcel forums, mechanisms for users to provide input to user-driven development and how feedback is provided, publicly available information of how to join the Ambassador Program and plan for its activities, and summary of selected external showcases.

Data Management Plan

The plan will be developed in accordance with EC guidelines regarding FAIR data management and will describe what and how data will be generated, collected, processed, curated and preserved during and after the end of the project.

Quality assurance and risk management plan

This deliverable will discuss the overall quality monitoring process for the project (such as deliverables and milestone completion, KPIs) and the overall risk management strategy. The risks will be regularly assessed in the mandatory management reports.

Publications

DeepRank-GNN-esm: A Graph Neural Network for Scoring Protein-Protein Models using Protein Language Model.

Auteurs: X. Xu, A.M.J.J. Bonvin
Publié dans: Bioinformatics Advances, 2023, ISSN 2635-0041
Éditeur: Oxford Academic
DOI: 10.1093/bioadv/vbad191

Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking.

Auteurs: M. Giulini, C. Schneider, D. Cutting, N. Desai, C. Deane and A.M.J.J. Bonvin
Publié dans: BioRxiv, 2023, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.11.17.567543

ARCTIC-3D: Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information

Auteurs: Marco Giulini; Rodrigo V. Honorato; Jesús L. Rivera; Alexandre M.J.J. Bonvin
Publié dans: Communication Biology, Numéro 7:49, 2024, ISSN 2399-3642
Éditeur: Springer Nature
DOI: 10.5281/zenodo.8131700

DeepRank-GNN: A Graph Neural Network Framework to Learn Patterns in Protein-Protein Interfaces

Auteurs: M.F. Réau, N.Renaud, L.C. Xue and A.M.J.J. Bonvin
Publié dans: Bioinformatics, 2023, ISSN 1367-4811
Éditeur: Oxford Academic
DOI: 10.1093/bioinformatics/btac759

Livrables

Publications

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