7th CAPRI evaluation meeting
EMBL-EBI, Hinxton, UK, April 3-5, 2019
- EMBL-EBI, Hinxton, UK, April 3-5, 2019
- About
- Sponsors
- Keynote speakers
- Program
- Venue
- Registration
- Accommodations
- Instruct-ERIC Workshop
- Registration
- Program
- Contact information
About
Get the latest update on the current status of computational procedures for modeling protein-protein interactions and the association of proteins with other macromolecules from this 7th CAPRI evaluation meeting. For more information - http://www.ebi.ac.uk/msd-srv/capri/
CAPRI (Critical Assessment of Predicted Interactions) is a community wide experiment designed to test methods for predicting the structure of macromolecular complexes based on the known structure of their components.
The meeting program will include an overview of the performance of protein docking and scoring procedures obtained for targets evaluated since the spring of 2013. It will also feature several plenary lectures by prominent scientists, as well as talks by the best CAPRI performers, and/or groups developing innovative computational approaches. CAPRI groups selected for oral representations will be notified, once the predictions for all outstanding targets have been completed.
We hope to see you all in Hinxton in April!
Sponsors
Keynote speakers
| Madan Babu (MRC Laboratory of Molecular Biology) |
Louise Walport (Francis Crick Institute) |
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| Todd O. Yeates (University of California, Los Angeles) |
John Jumper (DeepMind Technologies, UK) |
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Program
Day 1
| 08:30 | Coach from Cambridge |
| 09:15 - 09:45 | Registration |
| Welcome Address | |
| 09:45 - 10:00 | Sameer Velankar (European Bioinformatics Institute) |
| Session 1: CAPRI Targets and Evaluation Results | |
| 10:00 - 10:50 | Marc Lensink (University of Lille, France) |
| CAPRI 2019 edition: Modeling a diverse landscape of protein complexes | |
| 10:50 - 11:20 | Shoshana Wodak (Free University of Brussels, Belgium) |
| Modeling protein-protein assemblies: The CASP13-CAPRI challenge | |
| 11:20 - 13:00 | Poster session and lunch |
| Session 2: Highlights from CAPRI Prediction Results and Methods I | |
| 13:00 - 13:20 | Alexandre Bonvin (Utrecht University, The Netherlands) |
| Data-driven HADDOCK strategies in CAPRI rounds 38-45 | |
| 13:20 - 13:40 | Dima Kozakov (Stony Brook University, USA) |
| ClusPro performance in CAPRI and the new methods | |
| 13:40 - 14:00 | Juan Fernandez-Recio (Barcelona Supercomputing Center, Spain) |
| Integrative modeling with pyDock for the new protein docking challenges in 7th CAPRI | |
| 14:00 - 14:20 | Daisuke Kihara (Purdue University, USA) |
| Human team and LZerD server pipeline for template-based and ab initio protein-protein interaction modeling |
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| 14:20 – 14:40 | Zhiping Weng (University of Massachusetts, USA) |
| Title TBC | |
| Keynote Lecture I | |
| 14:40 – 15:30 | Madan Babu (MRC Laboratory of Molecular Biology, UK) |
| Title TBC | |
| 15:30 - 15:50 | Coffee break |
| Session 3: New approaches to sampling interactions | |
| 15:50 - 16:10 | Martin Zacharias (Technical University of Munich, Germany) |
| Refinement and evaluation of docked protein-protein complexes using coarse-grained and atomistic models in ATTRACT |
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| 16:10 - 16:30 | Maria Elisa Ruiz Echartea (University of Lorraine, France) |
| EROS-DOCK for Pairwise and Multi-body Protein-Protein Docking | |
| 16:40 - 16:55 | Paul Bates (The Francis Crick Institute, UK) |
| Exploring Conformational Search Strategies for Protein Targets Displaying a Wide Range of Conformational Change upon Protein-Protein Complex Formation |
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| 16:50 – 17:10 | Jeffrey Gray (Johns Hopkins University, USA) |
| Novel sampling strategies and a coarse-grained score function for docking homomers,flexible heteromers and oligosaccharides using Rosetta in CAPRI |
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| 17:20 – 18:10 | Flash talks for poster presenter |
| 18:10 – 20:00 | Poster Session and Buffet |
Day 2
| 08:30 | Coach from Cambridge |
| Keynote Lecture II | |
| 09:30 - 10:20 | Louise Walport (The Francis Crick Institute, UK) |
| A RaPID approach to inhibiting protein-protein interactions | |
| 10:20 - 10:40 | Coffee break |
| Session 4: Highlights from CAPRI Prediction Results and Methods II | |
| 10:40 - 11:00 | Li Xue (Utrecht University, The Netherlands) |
| iScore: A novel graph kernel-based function for scoring protein-protein docking models | |
| 11:00 - 11:20 | Yang Shen (Texas A&M University, USA) |
| Bayesian Active Learning for Optimization and Uncertainty Quantification in Protein Docking |
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| 11:20 - 11:40 | Didier Barradas-Bautista (King Abdullah University of Science and Technology, Saudi Arabia) |
| How we ranked high/medium quality models at the Top-1 position for 11 targets in CASP13-CAPRI46 |
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| 11:40 - 12:00 | Raphaël Guerois (Université Paris‐Saclay, France) |
| Docking Proteins and Peptides Under Evolutionary Constraints | |
| 12:00 - 14:00 | Poster session and lunch |
| Keynote Lecture III | |
| 14:00 - 14:50 | Todd O. Yeates (University of California, Los Angeles, USA) |
| Designed protein assemblies: intersections with problems in geometry and docking | |
| 14:50 - 15:10 | Coffee break |
| Session 5: Beyond docking: affinity, mutation and non-specific interactions | |
| Chair: Marc Lensink | |
| 15:10 – 15:30 | Michael J E Sternberg (Imperial College London, UK) |
| Identification of the structural impact of missense variants in experimental and predicted protein binary complexes |
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| 15:30 - 15:50 | José A. Villegas (Weizmann Institute of Science, Israel) |
| An asymmetric pairwise potential unifies amino acid interaction propensity with desolvation energy and reveals how surface and interior contribute to binding affinity |
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| 15:50 - 16:10 | Anne Lopes (Université Paris‐Saclay, France) |
| Protein interaction energy landscapes are shaped by functional but also non-functional partners |
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| 16:10 - 16:30 | Coffee break |
| Session 6: Protein-peptide docking | |
| Chair: Michael J. E. Sternberg | |
| 16:30 - 16:50 | Ora Schueler-Furman (Hebrew University of Jerusalem, Israel) |
| Peptide-protein binding via beta-sheet augmentation | |
| 16:50 - 17:10 | Xiaoqin Zou (University of Missouri, USA) |
| MDockPeP2: Predicting protein-peptide complex structures by accounting for peptide flexibility in long peptides |
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| Round Table Discussion | |
| 17:10 - 18:40 | The Future Protein Complex Modelling and CAPRI |
| Moderator: Shoshana Wodak | |
| 18:50 | Bus to Homerton College, Cambridge |
| 19:20 - 22:00 | Conference dinner. Homerton College |
Day 3
| 08:30 | Coach from Cambridge |
| 09:30 - 10:20 | Poster Session |
| 10:20 - 10:40 | Coffee break |
| Session 7: Template and symmetry based docking | |
| Chair: Alexandre Bonvin | |
| 10:40 - 11:00 | Ilya A Vakser (The University of Kansas, USA) |
| Interface vs. Full Structure Similarity for Protein Docking | |
| 11:00 - 11:20 | Chaok Seok (Seoul National University, Republic of Korea) |
| Structure Prediction of Biological Assemblies using GALAXY in CAPRI rounds 38-45 | |
| 11:20 - 11:45 | Česlovas Venclovas (Vilnius University, Lithuania) |
| Template-based modeling using the PPI3D web server in CAPRI Rounds 38-45 | |
| 11:40 – 12:00 | Sergei Grudinin (Inria/CNRS, Grenoble, France) |
| Symmetry in Protein Complexes | |
| 12:00 - 13:13 | Lunch |
| Keynote Lecture IV | |
| 13:30 - 14:20 | John Jumper (DeepMind Technologies, UK) |
| AlphaFold: Improved protein structure prediction using potentials from deep learning | |
| Session 8: Combining traditional and template based modelling | |
| Chair: Paul Bates | |
| 14:25 - 14:45 | Ren Kong (Jiangsu University of Technology, China) |
| Template-based modeling and ab-initio docking using CoDock in CAPRI | |
| 14:45 - 15:05 | Arne Elofsson (Stockholm University, Sweden) |
| Using template and contact based docking in CAPRI 46 | |
| 15:05 - 15:20 | Meeting closing remarks |
| 15:20 - 15:40 | Coffee break |
| 15:40 | Shuttle to Cambridge |
| 16:30 | Punting tour (optional) |
Venue
EMBL-EBI, Hinxton, UK
European Bioinformatics Institue, EMBL-Outstation
Wellcome Trust Genome Campus
Hinxton, Cambridgeshire
CB10 1SD
United Kingdom
Registration
Registration for the 7th edition of the CAPRI evaluation meeting in Hinxton is open.
The registration fee for participants is set to £260 which includes:
3 days of scientific sessions including coffee-breaks and lunch on Wednesday, Thursday and Friday
Ongoing access to the poster area
Certificate of attendance
Conference dinner
All participants (excluding keynote speakers) are requested to pay the registration fee. Depending on availability of funds, a contribution towards travel and accommodation expenses will be provided to the selected speakers and plenary lecturers. Speakers will be notified by e-mail regarding the reimbursement policy.
Registration fee should be paid no later than 8 March 2019.
Accommodation is not included in the registration fee, but we have listed our recommendations for several hotel options in Cambridge.
Registrations are now closed.
Abstract Submission
Important guidelines for participants
A one page Abstract should be submitted for both oral and poster presentations. The deadline for Abstract submission is set to March 3 2019. Selected speakers will be notified by March 11 2019. Please email your abstract in Microsoft word format to info@bioexcel.eu.
Following the tradition of the meeting, the selected speakers will also be invited to contribute to the special issue of Proteins dedicated to CAPRI that will be published late 2019. Participants who apply for a regular talk should thus present work that is publishable and agree to contribute a manuscript for the Proteins special issue.
Accommodations
Accommodation is not provided for this event. Attendees are requested to arrange their own if required. It is strongly advised to book accommodation a month in advance as room prices tend to increase substantially closer to the date.
Staying on-site (Hinxton)
If you wish to stay in Hinxton, we recommend using the onsite accommodation - Wellcome Genome Campus Conference Centre. Book early as space is limited.
Hinxton Hall, Wellcome Genome Campus
Tel: +44(0) 1223 495 000
Fax: +44(0) 1223 495 114
conference.reception@wellcomegenomecampus.org
Central Cambridge
Holiday Inn Express Cambridge
15-17 Coldhams Park, Cambridge
Tel: +44 0871 902 1605
info@expresscambridge.co.uk
ibis Cambridge Central Station
2 Station Square, Cambridge
Tel: (+44)1223320960
Travelodge
Cambridge Leisure Park, Clifton Way, Cambridge
Tel: +44 (0)871 984 6101
AirBnB
Airbnb is a trusted community marketplace for people to list, discover, and book unique accommodation around the world. Visit https://www.airbnb.com for more information.
Coach Service
There will be a free bus service organised to/from the venue in Hinxton to multiple stops in Cambridge. The pick up and drop off points in Cambridge are - Grafton Centre, Cambridge railway station and Mowbray road. Specific details will be sent closer to the date.
Instruct-ERIC Workshop
Registration now open for the Joint Instruct-ERIC/CAPRI Workshop on Integrated Modelling of Protein-Protein Interactions Workshop. The course will run prior to the 7th CAPRI Assessment Meeting, from the 1st - 2nd April 2019 at EMBL-EBI, Hinxton, UK.
The course will consist of six sessions followed by a practical component overseen by the lecturer and an additional tutor. During the computer practicals, participants will learn to use and apply the various software with either their own data/structures, or with examples provided by the instructors.
Registration
Registration is free for participants from Instruct-ERIC countries and £250 from other countries. Visit the website to find out if you are from a participating Instruct-ERIC country. https://instruct-eric.eu/countries
Note: If you are from an Instruct-ERIC country, please select the option ‘I will pay later’ at the payment stage to register for free.
Accommodation is not included in the registration fee.
Program
Day 1 - 1st April 2019
| 11:10 | Coach from Cambridge Station |
| 12:00 - 13:00 | Registration and Lunch |
| 13:00 - 15:00 | Introduction to protein-protein docking: sampling and scoring |
| Practical: Flexible docking with SwarmDock | |
| Paul A. Bates, and Raphael A.G. Chaleil, Francis Crick Institute, London, UK | |
| 15:00 - 15:30 | Coffee Break |
| 15:30 - 17:30 | Integrative structure determination of macromolecular assemblies |
| Practical: Determination of macromolecular structure using Cryo-EM data | |
| Maya Topf and Sony Malhotra, Institute of Structural and Molecular Biology, London, UK | |
| 18:00 | Dinner |
Day 2 - 2nd April 2019
| 08:00 | Coach from Cambridge |
| 09:00 - 11:00 | Introduction to data-driven docking |
| Practical: Integrative docking with HADDOCK | |
| Alexandre M.J.J. Bonvin and Panos Koukos, Bijvoet Center for Biomolecular Research, Utrecht, NL | |
| 11:00 - 11:15 | Coffee Break |
| 11:15 - 13:15 | Protein-protein binding affinities |
| Practical: Modelling interaction strength using machine learning | |
| Iain H. Moal, EMBL European Bioinformatics Institute, Cambridge, UK | |
| 13:15 - 14:00 | Lunch |
| 14:00 - 16:00 | Protein structure prediction |
| Practical: Modelling protein structures and variants: Phyre, PhyreRisk, Missense3D and EzMol | |
| Michael J.E. Sternberg, Lawrence Kelley and Charles Tochukwu, Imperial College London, London, UK | |
| 16:00 - 16:15 | Coffee Break |
| 16:15 - 18:15 | The validation and verification of protein structure |
| Practical: Hands-on assessment of structural quality | |
| Gerard Kleywegt, EMBL European Bioinformatics Institute, Cambridge, UK | |
Coach Service
There will be a free bus service organised to/from the venue in Hinxton to Cambridge Station. Specific details will be sent closer to the date.
Contact information
Michelle Mendonca - mmendonca@ebi.ac.uk - +44 (0) 1223 494335