Alexandre Bonvin bio photo

CAPRI communitywide experiment on the comparative evaluation of protein-protein docking for structure prediction

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7th CAPRI evaluation meeting

EMBL-EBI, Hinxton, UK, April 3-5, 2019


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 -

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!




Keynote speakers

Madan Babu
(MRC Laboratory of Molecular Biology)
Louise Walport
(Francis Crick Institute)
drawing drawing
Todd O. Yeates
(University of California, Los Angeles)
John Jumper
(DeepMind Technologies, UK)
drawing drawing


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
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
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
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
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
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
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
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
15:50 - 16:10 Anne Lopes (Université Paris‐Saclay, France)
  Protein interaction energy landscapes are shaped by functional
but also non-functional partners
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
  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)


EMBL-EBI, Hinxton, UK

European Bioinformatics Institue, EMBL-Outstation
Wellcome Trust Genome Campus
Hinxton, Cambridgeshire
CB10 1SD
United Kingdom


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

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.


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

Central Cambridge

Holiday Inn Express Cambridge
15-17 Coldhams Park, Cambridge
Tel: +44 0871 902 1605

ibis Cambridge Central Station
2 Station Square, Cambridge
Tel: (+44)1223320960

Cambridge Leisure Park, Clifton Way, Cambridge
Tel: +44 (0)871 984 6101


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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 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.

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.

Register Now »


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 - - +44 (0) 1223 494335