Course at EMBL-EBI
3D-BioInfo community annual meeting
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 (https://www.elixir-europe.org/use-cases).
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?
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|
|13:45-15:15||Breakout sessions||See below|
|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|
|12:20-12:40||Galaxy session||Lee Larcombe|
|12:40-13:00||ELIXIR bio.tools||Jerry Lanfear|
|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 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|
|15:45-15:55||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|
|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:
||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|
|15:45-16:00||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|
|15:45-16:00||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: //www.ebi.ac.uk/about/contact.
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.