BioExcel 2nd SIG Meeting: “Advanced Simulations for Biomolecular Research” @ ECCB 2018


SIG BioExcel is a major venue for knowledge exchange and networking for the computational biomolecular research community. It brings together stakeholders of 1) core applications that are supported by the center – HADDOCK (integrative modelling), GROMACS (molecular dynamics simulations) and CPMD (hybrid QM/MM methods) and 2) worklow environments and platforms for data integration and analysis such as CWL, Galaxy, Taverna, Open PHACTS, COMPSs. These include:

  • Academic scientists whose research depends heavily on software for biomolecular simulations (e.g. users and developers)
  • Industrial users of such software, especially from pharmaceutical, chemical or food industries
  • Independent software vendors of biomolecular modeling/simulation applications or platforms
  • Resource providers for biomolecular simulations (HPC centers, commercial Cloud/HPC/Grid system providers)
  • International projects and initiatives in the area of biomolecular simulations

This year’s meeting will take place as a satellite event during ECCB2018 on 8th September in Athens.  The event will host invited talks by top-scientists, industrial (pharma) representatives, flash presentations of the highest quality abstracts from the poster session, and lunchtime hands-on presentation of cutting-edge high-end systems.

The venue will provide opportunities to participants to:

  • Showcase their success stories (posters and selected flash talks)
  • Discuss upcoming challenges and how they might be addressed
  • Share experience and best practices to develop standards
  • Create networking and collaboration opportunities with each other
  • Provide input into the development of improved software and workflows

Each edition of the SIG is organized in collaboration with local representatives of the computational biomolecular researchers. The second edition of the SIG is a joint event with Vi-SEEM ( as representatives of the Life Sciences Research community in the Southeast Europe and Eastern Mediterranean (SEEM) region. VI-SEEM provides scientists with access to state of the art virtual platform while integrating the underlying e-Infrastructure layers with generic/standardised as well as domain-specific services. It also promotes capacity building, fosters interdisciplinary approaches, and provides adequate user support and training programmes for the user communities in the SEEM region.


The SIG invites contributions for poster presentations and flash talks on all topics related to computational biomolecular research, including, but not limited to:

  • methods and algorithms for atomistic modelling and simulations
  • docking and integrative modelling
  • high-performance (HPC) and high-throughput (HTC) techniques and methods
  • ab initio and hybrid QM/MM methods for biomolecular systems modelling
  • coarse grained and multi-scale simulation methods
  • workflows and platforms for biomolecular simulations and data integration
  • distributed systems for modelling and simulations
  • data management for biological sciences – formats, databases, repositories, integration
  • industrial applications of biomolecular modelling and simulation
  • computer aided drug design
  • virtual screening
  • free energy calculations
  • use cases of HADDOCK, CPMD, GROMACS and other modelling and simulation applications
  • training and education in biomolecular modelling and simulation

Remember to submit your abstract before the deadline!

NOTE: The flashtalk deadlines have now expired however poster abstracts should be submitted to BioExcel for evaluation using the form at the bottom of this page according to the following deadlines:

Late poster only deadline: August 26th, 2018
NOTE: Poster submissions after 22nd July are not eligible for travel grants.

Travel bursaries

All applications for travel grants have now expired. For any further information please contact us at

Keynote Speakers

Jean-Pierre Changeux is an eminent biologist and neuroscientist and held the Chair for Cellular Communication at the Collège de France for thirty years. With the models he developed since the early 1970s for the selective stabilization and regression of synapses Changeux has made an important contribution to the research on neuroplasticity and processes of epigenesis. In his own words, it is this epigenetic flexibility that ensures, within the genetic envelope, the opening of the brain “to the physical, social, and cultural world”. Since his 1983 book L’Homme Neuronal (Neuronal Man) Changeux has increasingly broadened his focus from the molecular and cellular levels to investigations of the neuronal bases of cognitive functions and consciousness. Not coincidentally, the ‘conscious neuronal workspace’ also plays an important role in his neuroaesthetic conception of art as a form of symbolic intersubjective communication.
Matteo Dal Peraro graduated in Physics at the University of Padua in 2000. He obtained his Ph.D. in Biophysics at the International School for Advanced Studies (SISSA, Trieste) in 2004. He then received postdoctoral training at the University of Pennsylvania (Philadelphia) under the guidance of Prof. M. L. Klein. He was nominated Tenure Track Assistant Professor at the EPFL School of Life Sciences in late 2007. His research at the Laboratory for Biomolecular Modeling (LBM), within the Interfaculty Institute of  Bioengineering (IBI), focuses on the multiscale modeling of large macromolecular systems.


Start End Title
Presenter name (Affiliation)
9:00 9:15 Introduction and Welcome

BioExcel Center of Excellence
Rossen Apostolov (KTH Royal Institute of Technology, SWEDEN)

9:15 9:20 VI-SEEM Virtual Research Environment

Zoe Cournia (Life Sciences Scientific Community Leader, VI-SEEM)

9:20 9:50 “Computer-aided drug design to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2”

Zoe Cournia (BRFAA, GREECE)

9:50 10:30 “Exploring protein-membrane interplay with molecule simulations”
Matteo Dal Peraro (EPFL, SWITZERLAND)
10:30 11:00 Poster session + networking coffee break
11:00 11:30 Flash talks selected from abstracts
11:30 12:00 “Automated Selectivity Inversion of Kinase Inhibitors”
Simone Fulle (Novonordisk)
12:00 12:30 Immersive visual exploration of biomolecular systems in virtual reality – from static views to interactive dynamics”
Marc Baaden (IBPC, FRANCE)
12:30 13:30 Lunch and demonstrations of VR (virtual reality) kit application for drug design
13:30 14:00 “Focussing the computational microscope on bacterial membranes”
Syma Khalid (University of Southampton, UK)
14:00 14:30 “Biosignatures – Large-scale machine learning for translating high-dimensional biological responses into drug design decisions”
Joerg Kurt Wegner (Janssen Pharmaceuticals)
14:30 15:00 Flash talks selected from abstracts
15:00 15:30 Poster session + networking
15:30 15:45 “Integrative modelling with HADDOCK: From solution to membranes”
Panagiotis Koukos (University Utrecht, The NETHERLANDS)
15:45 16:10 “From (Big) Data to Value in Drug Discovery: Surfing on the Data Lake”
George Papadatos (GSK)
16:10 17:00 KEYNOTE SPEECH
Jean-Pierre Changeux (Pasteur Institute)
17:00 17:05 Closing remarks

NOTE: If you are unable to join our workshop’s then please head down to our booth. We will have representatives of the BioExcel CoE throughout the day and the chance to use our VR Kit!

Important Dates

BioExcel SIG deadlines

Abstract submission for flashtalk’s as well as applications for travel bursaries have now expired. Poster submissions are still oen until the deadline below.

Late poster only deadline: August 26th, 2018
NOTE: Poster submissions after 22nd July are not eligible for travel grants.

ECCB Registration deadlines

Early-bird registration deadline: July 29, 2018
Registration online deadline : August 31, 2018
Workshop Date: September 8, 2018


SIG BioExcel is a satellite meeting of ECCB’18 and registration should be done through

IMPORTANT: Make sure to register for the SIGs/Workshops at the above address! Registering for the main conference only will _NOT_ let you attend the pre-meetings. The fees are below.

Fees for workshops/special interest group meetings during the pre-meetings (8 & 9 September)

category early late on-site
1 day – academic/industry 110 165 190
1 day – MSc/PhD student 60 90 115
2 days – academic/industry 180 270 295
2 days – MSc/PhD student 100 150 185


  • Rossen Apostolov, KTH, Sweden
  • Zoe Cournia, BRFAA, Greece
  • Vera Matser, EMBL-EBI, UK
  • Anastas Mishev, UKIM, Macedonia
  • Hrachya Astsatryan, IIAP, Armenia
  • Adam Carter, EPCC, UK


Abstracts should be sent through the form below and may include published or already submitted material to other conferences, workshops or journals.

Full Name (required)

Institution (required)

Email (required)

Abstract (max 500 words)

Alternatively, attach a file (1MB size limit):

Additional information

If you have any questions regarding the SIG meeting, please contact us at

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08 Sep, 2018
All Day

Stavros Niarchos Foundation Cultural Center (SNFCC)


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