Course at EMBL-EBI

3D-BioInfo community annual meeting

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ELIXIR Communities enable the participation of communities of practice in different areas of the life sciences in the activities of ELIXIR, which underpin the evolution of a data, tools, interoperability, compute and training infrastructure for European life science informatics (

Structural bioinformatics has a broad impact across the life sciences and provides tools to archive, visualise, analyse, annotate, and predict the structure of biological macromolecules. Structural bioinformatics is traditionally very strong in Europe offering many software tools, methodologies, and databases, as well as community-wide prediction challenges.

Its applications cover research activities from structural biology to drug discovery and personalised medicine that are all well represented within the national ELIXIR nodes.

The 3D-BioInfo Community was approved by ELIXIR in May 2019. This meeting will be the first official meeting of the community to plan major activities and to identify research groups wishing to contribute to these activities.

Who is this course for?

This workshop is aimed at members and collaborators of the 3D-BioInfo Community.

What will I learn?

Learning outcomes

This workshop will help the 3D-BioInfo Community plan their major activities and identify research groups willing to contribute towards these activities.


Day 1 – Thursday 21 November 2019
11:00 Shuttle from Cambridge Station (Stop 5)  
11:30 Arrival and registration  
12:00-12:20 Overview of 3D-Bioinfo activities Christine Orengo
12:20-12:30 Infrastructure for FAIR structural and functional annotation Sameer Valendar
12:30-12:40 Open resources for sharing, integrating and benchmarking software tools for modelling the proteome in 3D Shoshana Wodak
12:40-12:50 Protein-ligand interactions Vincent Zoete
12:50-13:00 Tools to describe, analyse, annotate, and predict nucleic acid structures Bohdan Schneider
13:00-13:45 Lunch  
13:45-15:15 Breakout sessions See below
15:15-15:45 Break  
15:45-17:15 Breakout sessions See below
17:15 End of day  
18:00 Evening meal Hinxton Hall Restaurant
20:00 Shuttle to Cambridge Station (Stop 5)  
Day 2 – Friday 22 November 2019
08:00 Shuttle from Cambridge Station (Stop 5)  
08:30 Arrival and registration  
09:00-10:00 Protein engineering; presentation and discussion Lynne Regan
10:00-11:00 Breakout reporting  
11:00-11:20 Break  
11:20-12:20 Breakout reporting  
12:20-12:40 Galaxy session Lee Larcombe
12:40-13:00 ELIXIR Jerry Lanfear
13:00-14:00 Lunch  
14:00-15:00 Keynote talk John Briggs
15:00-16:00 Interaction with Instruct ERIC discussion  
16:00-16:15 Wrap up Christine Orengo
16:30 Shuttle to Cambridge Station (Stop 5)  

Breakout sessions

Breakout 1: Infrastructure for FAIR structural and functional annotations
13:45-13:55 Introduction and background Sameer Valankar
13:55-14:25 PDBe-KB progress and plans Mihaly Varadi
14:25-14:35 Benchmarking CATH FunSites Christine Orengo
14:35-14:45 Thoughts on benchmarking of ligand binding sites Mark Wass
14:45-14:55 Functional site annotation and benchmarking from structure-based function predictions Tomasz Kosciolek
14:55-15:15 Discussion: Benchmarking data sets for assessment of predicted functional sites Moderator: Geoff Barton
15:15-15:45 Break  
15:45-15:55 3D Beacons plan Sameer Velankar
15:55-16:10 Benchmarking the structural impact of missense variants in PDB and predicted structures Mike Sternberg
16:10-16:30 SWISS-MODEL: Model quality and lessons learned from user requests Stefan Bienert
16:30-17:15 Discussion: “Confidence” measures consensus predicted models Moderator: Christine Orengo
Breakout 2: Open resources for sharing, integrating and benchmarking software tools for modelling the proteome in 3D

Tools for characterizing and annotating the structures of protein complexes: Available tools, their complementarities and overlaps; what are we missing?

13:45-13:55 Introduction and background Shoshana Wodak
13:55-14:05 Web-based resources to model and benchmark protein interaction networks and multiprotein complexes Patrick Aloy
14:05-14:15 Analysis, comparison and assessment of proteins and protein complexes using interatomic contact areas instead of distances Ceslovas Venclovas
14:15-14:25 To be confirmed Ronald Dunbrack
14:25-14:35 PiQSi, QSalign, and QSbio: identifying biologically relevant protein assemblies in the PDB based on sequence-structure similarity relationships Emmanuel Levy
14:35-15:15 Discussion: How to leverage existing resources/tools for characterising macromolecular complexes in the PDB; what are we missing? Moderator: Alexandre Bonvin
15:15-15:45 Break  
Defining standards and workflows for characterizing different versions of the same complex; functionally relevant assembly modes; other?
15:45-15:55 Benchmark development and assessment for free docking applications using homology models Jessica Andreani & Raphael Guerois
15:55-16:05 Computational characterization of quaternary structure and function Ilya Vakser
16:05-16:15 Analysis of complexes in the PDB John Berrisford
16:15-16:25 Strongly interoperable workflows for structural bioinformatics Sjoerd de Vries
16:25-16:35 Towards validating protein-protein interfaces in hetero-oligomer assemblies Jürgen Haas
16:35-17:15 How to organize ourselves in practice:
  • What would be the initial set of tools?
  • Can we agree on workflows to be evaluated?
  • How do we go about defining/building a limited – proof of concept-benchmark dataset of ‘true exam- ples’ of protein-complexes?
Moderator: Shoshana Wodak
Breakout 3: Protein-ligand interactions
13:45-14:00 Introduction and background Vincent Zoete
14:00-14:15 Actual and future content of PDBe Lukas Pravda
14:15-14:30 Leveraging the PDB validation pipeline to select reliable ligand-biomacromolecule benchmarking targets Xavier Robin
14:30-14:45 Physico-chemical properties of small molecules and online visualization of 3D structures Radka Svobodova
14:45-15:15 Discussion Moderator: Pierre Tuffery
15:15-15:45 Break  
15:45-16:00 ProteinsPlus: Modern Algorithms for structure-based design studies on the web Katrin Schöning-Stierand
16:00-16:15 Protein structural statistics with PSS/application to ligand binding sites Roland Stote
16:15-16:30 Future needs in structure-based CADD Marcel Verdonk
16:30-16:45 The PDB-REDO databank as a resource for ligand structures and ligand validation metrics Perrakis Anastassis
16:45-17:15 Discussion and planning session Moderator: Vincent Zoete
Breakout 4: Tools to Describe, Analyse, Annotate, and Predict Nucleic Acid Structures
13:45-14:00 Welcome and background Bohdan Schneider
14:00-14:15 Introduction and framework Eric Westhof
14:15-14:30 RNA 3D structure modeling methods Janusz Bujnicki
14:30-14:45 Tools available for RNA modeling Jan Gorodkin
14:45-15:00 Simulation and bioinformatics approaches to the description of nucleic acids Modesto Orozco
14:45-15:15 RNA Puzzles Chichau Miao
15:15-15:45 Break  
15:45-16:00 Nucleic acid tools in the X-ray community: where do we stand? Robbie P. Joosten
16:00-16:15 Overview of geometry standards for nucleic acid structures Bohdan Schneider
16:15-16:30 Initiation of the general discussion Eric Westhof
16:45-17:15 Discussion: Setting future goals, setting topic & venue of the next NA-oriented meeting Moderator: Bohdan Schneider

Attendance at this workshop is allocated on a first come, first served basis.

The registration fee covers your lunch, refreshments, the workshop dinner and a shuttle between Cambridge Station (Stop 5) and the Wellcome Genome Campus. Accommodation is not included and you will need to make your own arrangements.

Please note that registration closes two weeks prior to the course, so please register as soon as you can. Once you have registered and we have received payment we can provide a letter of support should you require a visa to travel to the UK. Applying for a visa can take several weeks, and it might not be possible to be granted a visa if you register just before the closing date. If you are unable to attend, then please notify us as quickly as possible so that we can offer your place to someone else.

Accommodation is not provided for this workshop and participants will need to arrange this for themselves. We reccommend booking at the Wellcome Genome Campus Conference Centre on site. Please book as early as you can as space can be limited. For other recommendations in the local area please see: //

If there is sufficient interest from participants we can arrange a shuttle between Station Road, Cambridge and the campus each day. This will be of use to Cambridge residents or visitors choosing to stay in the city for the duration of the workshop.

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21 - 22 November 2019
European Bioinformatics Institute United Kingdom
Charlotte Pearton

  • Sameer Velankar
  • Christine Orengo
    University College London, UK
  • Tom Hancocks

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