3D-Gateway to protein structure and function

Lead Research Organisation: European Bioinformatics Institute
Department Name: MSCB Macromolec, structural and chem bio

Abstract

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Technical Summary

Despite significant advances in protein structure determination, the majority of proteins have no experimental structural data. Significant improvements in structure prediction methods can fill this gap and provide valuable data for understanding protein functions. Presently, structure data are archived in distinct resources (the PDB for experimental structures, and Genome3D and other specialist resources for predicted models) impeding their access by the wider user community. The 3D-Beacons infrastructure will allow seamless access to all structure models providing a mechanism for maximising structural coverage of UniProtKB.

The 3D-Beacons network will also simplify the comparison of models from different model repositories, allowing development of better confidence measures. Collaboration of resources will ensure the sustainability of the system, and the proposed uniform data access mechanism (REST API) will simplify integration of structural data by other resources such as InterPro and Ensembl and tools such as JalView, Chimera, Pymol to provide an essential foundation for understanding the impacts of genetic variations on protein functions. Access to model structures is also valuable in structure determination and analysis pipelines.

We will also develop mechanisms for transferring structure-based functional annotations from the PDBe Knowledgebase to UniProt proteins, and derive a confidence measure for the annotations. This infrastructure will allow integration and display of these annotations for UniProt sequences from key model organisms including important agricultural organisms and their pathogens.

Furthermore, these functional annotations will be built into the UniProt UniRule system enabling both (i) large scale annotation of the UniProt KnowledgeBase (UniProtKB) and (ii) their use by other groups annotating completed genomes or metagenome data, through the UniFIRE (the UNIprot Functional annotation Inference Rule Engine) system.

Planned Impact

Protein structure data provides valuable insights into the mechanisms by which proteins function and can thus provide explanation for impacts of genetic variation. It also aids drug design and protein engineering e.g. for greater stability or higher catalytic efficiency. The impact of structural data is evident from the significant uptake of the data by the community. For example, structural data in PDBe is accessed by >60,000 unique users/month. Genome3D is an integrated resource with structural data from 5 world-leading UK resources, whose sites typically attract 10,000 - 15,000 users/month. The Genome3D data is also disseminated via InterPro which has 135,000 unique users/month.

Despite significant advances in protein structure determination, a significant proportion of proteins have no experimental structural data in the PDB. However, protein structure prediction methods have improved significantly and the models produced can provide valuable data for understanding protein functions and the impacts of genetic variations. By expanding the predicted structural data in Genome3D and implementing the 3D-Beacon network to integrate additional predicted data from other internationally acclaimed resources (i.e. ModBase, Rosetta, SWISS-MODEL), we will maximise the structural coverage of sequences in UniProtKB and provide valuable data benefitting a very wide community of biologists. As well as aggregating known/predicted structural data, 3D-Beacon network will aggregate structure-based functional annotations from PDBe-KB. Our 3D-Gateway pages will be carefully designed to display all this information for a given UniProt sequence, in a highly intuitive manner that makes the source of, and confidence in, the data clear. The impact of UniProt in the biological community is extremely high, with access by >750,000 biologists each month.

Our project has clear deliverables likely to have impact on research studies:
(1) 3D-Beacon network based aggregation of structural and functional data will also allow individual groups to download aggregated structural data for sets of UniProt proteins. This gives a mechanism for other data providers, e.g. Interactome3D, to combine the data with their information, e.g. on protein interactions and drug targets.
(2) Dedicated 3D-Gateway webpages showing structural and functional annotations will provide biologists access to functional information on a protein they are studying. In this context information provided by UniProt on known disease variants will be enriched by structural and functional information, provided by our 3D-Gateway project, highlighting key residues.
(3) The incorporation of structural and functional annotations in UniRules will allow safe transference of annotations to an even greater set of UniProt sequences and these rules will also be available to genome curators to enable functional annotation and comparative genome studies.

Industry will also benefit from the structural and functional annotations of UniProt sequences on the 3D-Gateway pages, to guide drug design.

As an activity in the ELIXIR Community of Structural Bioinformatics, 3D-Beacons will make the aggregated data available to groups across Europe and beyond, who in turn will contribute their own data to 3D-Beacons for display on the web pages. This community will also be involved in exploring mechanisms to ensure the quality of the aggregated data (e.g. by highlighting outlying data and developing sound confidence measures).

Furthermore, the ELIXIR 3D-BioInfo Community is building links with the ELIXIR Rare Disease and Galaxy Communities to develop workflows for accessing known and predicted structural data. ELIXIR funding is already supporting development of web-based training workflows in TESS, by PDBe and Genome3D, for exploiting structural data to gauge the impacts of genetic variations. This training material will ensure wider uptake and exploitation of data from the 3D-Gateway project.
 
Description Recent structure prediction advances have resulted in several data resources making high-quality structure models available (e.g. AlpahFold Database, Model Archive, AlphaFill etc.). Traditionally several data resources made experimentally determined structure models publicly available (e.g. PDB, SASBDB, PED etc.). With the increasing fragmentation of data, it was essential to devise a mechanism to provide access to all these resources using a common mechanism. This project brought the data archives teams together and developed a common standard and platform for accessing structure data.
Exploitation Route The software design developed in this project could provide a mechanism to integrate access to disparate sources on the web providing similar types of data. The approaches developed could also provide a blueprint for bringing different actors together to agree on common standards for data representation and access. This could be of help in developing ways to access healthcare and research data from different sources in a scalable system.
Sectors Healthcare

Pharmaceuticals and Medical Biotechnology

URL https://3d-beacons.org
 
Title 3D-Beacons API specification 
Description The 3D-Beacons API specification is a data exchange model for experimentally determined and theoretical macromolecular structures. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact This specification is essential to ensure interoperability and reusability of 3D-Beacons data which is made accessible through the 3D-Beacons Network. 
URL https://3dbeacons.docs.apiary.io/#
 
Title Supporting data for "3D-Beacons: Decreasing the gap between protein sequences and structures through a federated network of protein structure data resources" 
Description While scientists can often infer the biological function of proteins from their 3-dimensional quaternary structures, the gap between the number of known protein sequences and their experimentally determined structures keeps increasing. A potential solution to this problem is presented by ever more sophisticated computational protein modelling approaches. While often powerful on their own, most methods have strengths and weaknesses. Therefore, it benefits researchers to examine models from various model providers and perform comparative analysis to identify models that best address their specific use cases. To make data from an extensive array of model providers more easily accessible to the broader scientific community, we established 3D-Beacons, a collaborative initiative to create a federated network with unified data access mechanisms. The 3D-Beacons Network allows researchers to collate coordinate files and metadata for experimentally determined and theoretical protein models from state-of-the-art and specialist model providers and also from the Protein Data Bank. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact Making the 3D-Beacons infrastructure open-source help providers of experimentally-determined and computationally predicted molecular structures and annotations to more easily make their data available through the 3D-Beacons Network. It also allows the community to suggest improvements to every element of the infrastructure in a transparent way. 
URL http://gigadb.org/dataset/102328
 
Description Collaboration on sharing variant models 
Organisation Centre for Genomic Regulation (CRG)
Country Spain 
Sector Academic/University 
PI Contribution We provide support for getting the 3D-Beacons infrastructure working for FoldX models.
Collaborator Contribution They provide models on variants using the 3D-Beacons infrastructure.
Impact Structural models of variants will be provided by FoldX using the 3D-Beacons infrastructure.
Start Year 2020
 
Description Collaboration with AlphaFill 
Organisation Netherlands Cancer Institute (NKI)
Country Netherlands 
Sector Academic/University 
PI Contribution We worked together with AlphaFill, a data resource in the Netherlands, to support them in making their modified AlphaFold predictions accessible via 3D-Beacons. We made adjustments to the 3D-Beacons schema to help them share their data.
Collaborator Contribution They implemented the 3D-Beacons API endpoints and linked their API to the 3D-Beacons Network.
Impact Their modified AlphaFold predictions are publicly available through the 3D-Beacons Network.
Start Year 2022
 
Description Collaboration with HegeLab 
Organisation Hungarian Academy of Sciences (MTA)
Country Hungary 
Sector Academic/University 
PI Contribution We worked together with HegeLab (http://www.hegelab.org/), a research group in Hungary, to support them in making their ABC protein family predictions accessible via 3D-Beacons. We made adjustments to the 3D-Beacons schema and the 3D-Beacons Client to help them share their data.
Collaborator Contribution The HegeLab took the 3D-Beacons Client and set it up at their site. They linked their "beacon" to the 3D-Beacons Network.
Impact We have a shared publication where our team at EBI are co-authors. See the publications section, Tordai Het al. (2022). Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology. International journal of molecular sciences, 23 (16)
Start Year 2022
 
Description Collaboration with Isoform.io 
Organisation Johns Hopkins University
Country United States 
Sector Academic/University 
PI Contribution We worked together with Isoform.io (https://isoform.io/), a data resource of a research group in the US, to support them in making their human isoform predictions accessible via 3D-Beacons. We made adjustments to the 3D-Beacons schema and the 3D-Beacons Client to help them share their data.
Collaborator Contribution They worked with us to make their data available through 3D-Beacons.
Impact No formal output yet other than having their predicted models accessible through the 3D-Beacons Network.
Start Year 2022
 
Description Levy Lab, a new 3D-Beacons Network member 
Organisation Weizmann Institute of Science
Country Israel 
Sector Academic/University 
PI Contribution The Levy Lab from the Weizmann Institute joined the 3D-Beacons network to make their models accessible via 3D-Beacons.
Collaborator Contribution They make their computationally predicted structures accessible via 3D-Beacons.
Impact Data accessible via 3D-Beacons, i.e. https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/
Start Year 2023
 
Description Protein Ensemble Database contributing ensembles to the 3D-Beacons network 
Organisation University of Padova
Country Italy 
Sector Academic/University 
PI Contribution We provide support for getting the PED conformational ensembles available via the 3D-Beacons infrastructure.
Collaborator Contribution They provide links and meta-information for PED entries that are made available via 3D-Beacons.
Impact Conformational ensembles are being made available via the 3D-Beacons network.
Start Year 2020
 
Title 3D-Beacons Client 
Description The 3D-Beacons Client is a lightweight Python package that allows researchers to link their in-house models to the 3D-Beacons Network. It takes PDB and/or mmCIF files as input and generates the necessary metadata which is then exposed through a set of API endpoints that comply with the 3D-Beacons data specifications. 
Type Of Technology Software 
Year Produced 2022 
Open Source License? Yes  
Impact 3D-Beacons Client provides various tools and infrastructure to make local structural models available to the 3D-Beacons network. 
URL https://github.com/3D-Beacons/3d-beacons-client
 
Title 3D-Beacons Hub API 
Description The 3D-Beacons Hub acts as an aggregator of data from the various members of the 3D-Beacons Network. It uses the 3D-Beacons Registry to look up which API endpoints are supported by which 3D-Beacons, retrieves the data, and collates it to present the combined metadata programmatically to users. 
Type Of Technology Webtool/Application 
Year Produced 2022 
Open Source License? Yes  
Impact 3D-Beacons Hub allows researchers to access model coordinate file (mmCIF or PDB format) and related meta-information using a set of defined API endpoints that comply with the 3D-Beacons data specifications. 
URL https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/
 
Title 3D-Beacons Registry 
Description The 3D-Beacons Registry contains information on which data providers are members of the 3D-Beacons Network, and which API specifications did they implement. This allows both the 3D-Beacons Hub and any users to find out what API endpoints are available from which data providers. For example, if users are only interested in getting data from SASBDB, they can check in the registry which API URLs they should use. 
Type Of Technology Software 
Year Produced 2022 
Open Source License? Yes  
Impact The 3D-Beacons Registry allows any potential data provider to join the 3D-Beacons Network. 
 
Title 3D-Beacons web pages 
Description 3D-Beacons is an open collaboration between providers of macromolecular structure models. This collaboration aims to provide model coordinates and meta-information from all the contributing data resources in a standardised data format, on a unified platform. The web pages provide access to all its functionalities. 
Type Of Technology Webtool/Application 
Year Produced 2022 
Open Source License? Yes  
Impact Users can access all the API endpoints, and thus all the data through using the 3D-Beacons web pages. 
URL https://3d-beacons.org
 
Description 3D-Beacons Hackathon August 2020 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The 4th 3D-Beacons virtual hackathon was open to any international participants.
Year(s) Of Engagement Activity 2020
 
Description 3D-Beacons Hackathon January 2021 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The 7th 3D-Beacons virtual hackathon was open to any international participants.
Year(s) Of Engagement Activity 2021
 
Description 3D-Beacons Hackathon January 2022 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The 11th virtual hackathon for the 3D-Beacons project, where the infrastructure and data exchange formats were further developed.
Year(s) Of Engagement Activity 2022
 
Description 3D-Beacons Hackathon July 2020 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The 3rd 3D-Beacons virtual hackathon was open to any international participants.
Year(s) Of Engagement Activity 2020
 
Description 3D-Beacons Hackathon June 2020 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The 2nd 3D-Beacons virtual hackathon was open to any international participants.
Year(s) Of Engagement Activity 2020
 
Description 3D-Beacons Hackathon March 2020 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The 1st 3D-Beacons virtual hackathon was open to any interested participants.
Year(s) Of Engagement Activity 2020
 
Description 3D-Beacons Hackathon March 2021 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The 8th virtual hackathon for the 3D-Beacons project, where the infrastructure and data exchange formats were further developed.
Year(s) Of Engagement Activity 2021
 
Description 3D-Beacons Hackathon November 2020 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The 6th 3D-Beacons virtual hackathon was open to any international participants.
Year(s) Of Engagement Activity 2020
 
Description 3D-Beacons Hackathon October 2020 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The 5th 3D-Beacons virtual hackathon was open to any international participants.
Year(s) Of Engagement Activity 2020
 
Description 3D-Beacons Hackathon October 2021 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The 10th virtual hackathon for the 3D-Beacons project, where the infrastructure and data exchange formats were further developed.
Year(s) Of Engagement Activity 2021
 
Description 3D-Beacons Hackathon September 2021 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The 9th virtual hackathon for the 3D-Beacons project, where the infrastructure and data exchange formats were further developed.
Year(s) Of Engagement Activity 2021
 
Description 3D-Beacons as a project for BioHackathon 2020 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The 3D-Beacons project was presented on the BioHackathon 2020 where participants contributed to discussions and development.
Year(s) Of Engagement Activity 2020
 
Description 3D-Beacons presentation to the ELIXIR Beacons Network 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact 3D-Beacons was presented to the ELIXIR Beacons Network to get insights and suggestions from them.
Year(s) Of Engagement Activity 2020
 
Description 3D-BioInfo Annual Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact PDBe-KB (FunPDBe, BioChemGraph, covariation-related works), 3D-Beacons and AlphaFold DB was presented at the 3D-BioInfo Annual Meeting 2021.
Year(s) Of Engagement Activity 2021
 
Description 3D-BioInfo community webinar series 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Webinar giving an overview of the 3D Beacons project
Year(s) Of Engagement Activity 2021
 
Description 6th European Crystallographic School 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation, introducing PDBe and PDBe-KB resources
Year(s) Of Engagement Activity 2021
URL https://akcongress.com/ecs6/
 
Description A presentation at National Institute of Immunology, Delhi 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact The presentation included information on the PDB archive management by the wwPDB and its associate members. It also described the work done at PDBe on enriching the macromolecular structure data with structural and functional annotations for complexes, domains and small molecule ligands. The impact of AlphaFold was discussed, and the infrastructure developments to support the use of predicted models were described.
Year(s) Of Engagement Activity 2024
URL https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&ved=2ahUKEwjj4Oero9-EAxXBTEEAHQGGDPgQ...
 
Description BioHackathon 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact 3D-Beacons was one of the projects of the 2021 BioHackathon with participants working on the data integration infrastructure.
Year(s) Of Engagement Activity 2021
 
Description Bringing molecular structure to life: 50 years of the PDB 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation of PDBe and PDBe-KB resources to make PDB data more accessible
Year(s) Of Engagement Activity 2021
URL https://www.embl.org/about/info/course-and-conference-office/events/pdb21-01/
 
Description British Crystallographic Association (BCA) 2021 meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presentation of recent improvements at PDBe-KB pages
Year(s) Of Engagement Activity 2021
 
Description CCP-EM Workshop 2022 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact During the CCP-EM Icknield Workshop, we presented the AlphaFold DB, PDBe-KB and the 3D-Beacons Network to around 30 PhD students and researchers.
Year(s) Of Engagement Activity 2022
 
Description CCP4 Study Weekend 2021 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presentation of recent improvements at PDBe-KB pages and Q&A about PDB data and deposition
Year(s) Of Engagement Activity 2021
URL https://ccp4sw2021.meeting-mojo.com/page/agenda
 
Description CCP4 Summer School in York 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Two sessions/lectures: (1) Structural bioinformatics touching on PDBe, PDBe-KB, 3d beacons, alphafolddb, and (2) PDBe deposition.
Year(s) Of Engagement Activity 2023
URL https://www.ccp4.ac.uk/schools/ccp4-summer-school/index.php
 
Description CCPBioSim workshop 2023 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact A workshop to introduce trainees to the resources we provide and help them understand how to learn more about them.
Year(s) Of Engagement Activity 2023
 
Description EBI Industry Programme Quarterly meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Giving a talk on the PDBe, PDBe-KB and AlphaFoldDB resources as part of the EBI industry programme quarterly meeting. This gives the opportunity to engage with industry people about our activities and how they can make use of our data to support discovery and industry.
Year(s) Of Engagement Activity 2024
URL https://www.ebi.ac.uk/industry/private/industry-quarterly-meeting/2024/03/march-2024-industry-progra...
 
Description EBI Structural Bioinformatics Course 2021 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Around 30 participants attended the PDBe-KB session of the EBI Structural Bioinformatics Course who learned about the 3D-Beacons Network and the annotations provided by PDBe-KB consortium members. The deposition system used to collect these annotations was developed as part of the FunPDBe project.
Year(s) Of Engagement Activity 2021
URL https://www.ebi.ac.uk/training/events/structural-bioinformatics2021/
 
Description EBI Summer School group projects session 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Course on how to use the PDBe and PDBe-KB web resources to access and interrogate structural biology data. The participants came from a variety of backgrounds. They also learned how to access these data via the PDBe(-KB)'s APIs, picking up Python programming skills in the process. Many of them found the programming section challenging due to little previous programming experience.
Year(s) Of Engagement Activity 2023
 
Description EBI/Sanger Seminar Series 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Talk describing projects for enriching structural data, explaining how it has enabled the development of PDBe-KB aggregated views
Year(s) Of Engagement Activity 2021
URL https://www.ebi.ac.uk/about/events/events/internal-seminar/2021/ebisanger-seminar-series-sameer-vela...
 
Description EIPP Bioinformatics Predocs Course 2021 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Training session with PhD students to introduce them to accessing PDB data at PDBe and PDBe-KB resources
Year(s) Of Engagement Activity 2021
 
Description ELIXIR 3D-BioInfo AGM 2022 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This presentation gave an overview of PDBe-KB, AlphaFold DB and 3D-Beacons to around 100 international attendees.
Year(s) Of Engagement Activity 2022
 
Description ELIXIR All-Hands meeting 2022 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Around 100 researcher and engineers attended this session at the ELIXIR All-Hands meeting, 2022. The presentation gave an overview of 3D-Beacons, and how to use this network to make data accessible, and how to access the structures.
Year(s) Of Engagement Activity 2022
 
Description EMBL-EBI Research Talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact 3D-Beacons was presented in the context of PDBe-KB during an EMBL-EBI Research Talk.
Year(s) Of Engagement Activity 2020
 
Description EMBL-EBI virtual Pavia workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Training session with PhD students to introduce them to accessing PDB data at PDBe and PDBe-KB resources
Year(s) Of Engagement Activity 2021
URL https://www.ebi.ac.uk/training/events/embl-ebi-workshop-university-pavia-2021/
 
Description EMBL-EBI workshop: The Open University, 2021 (Virtual) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact Presentation, introducing PDBe and PDBe-KB resources
Year(s) Of Engagement Activity 2021
 
Description Hot Topics in Contemporary Crystallography course - Access and interpretation of structural biology data 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact A workshop to introduce trainees to the resources we provide and help them understand how to learn more about them.
Year(s) Of Engagement Activity 2023
URL https://htcc5.org/
 
Description Infection Biology Retreat 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact PDBe-KB, 3D-Beacons and the AlphaFold DB was presented at the EMBL Infection Biology Retreat in the context of infectious diseases.
Year(s) Of Engagement Activity 2021
 
Description Interpreting the effects of genetic variants on protein structure and function 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact A joint workshop with other EMBL-EBI resources to introduce a workflow to support understanding and interpretation of variants.
Year(s) Of Engagement Activity 2023
URL https://www.ebi.ac.uk/training/events/interpreting-effects-genetic-variants-protein-structure-and-fu...
 
Description King's College Structural Seminar Series 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Presentation, introducing PDBe-KB resources
Year(s) Of Engagement Activity 2021
 
Description Online workshop during ECCB 2020 "ELIXIR | 3D-Bioinfo: Integrating structural and functional data to support in silico predictions in drug design" 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The 3D-BioInfo Community aims to increase interoperability between resources by developing and promoting data standards, integrating data where appropriate and developing robust benchmarking strategies for prediction algorithms (e.g. protein structures, complexes, ligand/drug docking). Two major activities are the integration of known and predicted functional site data (e.g. ligand binding and protein interface residues) and protein ligand docking. In the first part of this tutorial students were taught how to access the site data in the PDBe Knowledge Base. The second part covered protein ligand interactions and drug design.

This workshop focused on PDBe-KB tools and the 3D-Bioinfo community, in collaboration with PDBe-KB partners.
Year(s) Of Engagement Activity 2020
URL https://eccb2020.info/ntbet01-3d-bioinfo-integrating-structural-and-functional-data-to-support-in-si...
 
Description PDBe-KB & 3D-Beacons presentation at Annual General Meeting of the 3D-BioInfo ELIXIR Community 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact PDBe-KB, 3D-Beacons and the covariation project were presented during the Annual General Meeting of the 3D-BioInfo ELIXIR Community.
Year(s) Of Engagement Activity 2020
 
Description PDBe-KB & 3D-Beacons presentation at Annual IDP Elixir Community Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented 3D-Beacons and PDBe-KB to the IDP ELIXIR Community during their annual meeting.
Year(s) Of Engagement Activity 2021
 
Description PSDI Virtual Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact PDBe-KB, with a focus on ligand-related work (i.e. BioChemGraph project), was presented to an audience of mainly drug discovery and development experts.
Year(s) Of Engagement Activity 2021
 
Description Presentation during the ELIXIR 3D-BioInfo community meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The first official meeting of the ELIXIR 3D-Bioinfo community to plan major activities and to identify research groups wishing to contribute to these activities.
Year(s) Of Engagement Activity 2020
URL https://www.ebi.ac.uk/training/events/3d-bioinfo-community-annual-meeting/
 
Description Seiminar at the Hungarian Bioinformatics Community seminar series 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Around 50 PhD students and postdoc researchers attended this seminar. The seminar gave an overview of 3D-Beacons and it's relation to PDBe-KB and the AlphaFold DB.
Year(s) Of Engagement Activity 2022
 
Description Seminar at MRC Toxicology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact This invited seminar at MRC Toxicology department gave an overview of AlphaFold DB, but also covered 3D-Beacons in the context of making AFDB models available. There were around 30 attendees.
Year(s) Of Engagement Activity 2022
 
Description Seminar in Prague about 3D-Beacons & AFDB 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact This invited seminar introduced 3D-Beacons, PDBe-KB and the AlphaFold DB, primarily to students of Charles University in Prague.
Year(s) Of Engagement Activity 2022
 
Description Structural bioinformatics course 2023 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact A workshop to introduce trainees to the resources we provide and help them understand how to learn more about them.
Year(s) Of Engagement Activity 2023
 
Description Workshop - Using machine learning to predict protein structures - Available resources and recommended practices for working with predicted models 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Short talk introducing PDBe-KB 3DBeacons and AlphaFoldDB and discussing recent updates, followed by hand-on- workshop with colab notebooks with various use-cases.
Year(s) Of Engagement Activity 2023