For each of our BioExcel training events we make a limited number of travel bursaries available. We ask the beneficiaries of the BioExcel travel grant to write a blog post for us, either about their experiences at the course, their research interests (in layman’s terms) or a relevant scientific topic.
SIG BioExcel is a major venue for knowledge exchange and networking for the computational biomolecular research community. The following posts are from travel beneficiaries who attended the 2018 SIG Meeting in Athens.

Stamatia Zavitsanou

Biomedical Research Foundation Academy of Athens

SIG BioExcel was a great opportunity for the computational biomolecular research community to get together. It hosted talks by top-scientists, industrial representatives, flash presentations of the highest quality abstracts from the poster session, and poster presentations of many projects from young researchers around the world. It was a joint event with Vi- SEEM as representatives of the Life Sciences Research community in the Southeast Europe and Eastern Mediterranean (SEEM) region.

Having myself a web-server hosted by Vi-SEEM, I could not miss the workshop. It was an honor, to have the chance to present my work as a flash talk, in front of these well-recognized scientists and thought fruitful discussion find ways to improve it even more.

In my talk an automated workflow for performing FEP/MD simulations was presented. One of the most important tasks in drug design is to predict, among a series of lead candidates, which ones will bind more strongly to the therapeutic target. In this direction, relative binding free energy methodologies have been developed, which rely on physics-based molecular simulations and rigorous statistical mechanics to calculate the differences in the free energy of binding between a parent candidate drug and analogs. For example, Free Energy Perturbation (FEP) calculations calculate the free energy difference between an initial (reference) and a final (target) molecule to an average of a function of their energy difference evaluated by sampling for the initial state.

Automating free energy perturbation calculations is a step forward to delivering high throughput calculations for accurate predictions of relative binding affinities before a compound is synthesized, and consequently save enormous time and cost. Computational methods in drug design have proven very useful as they render the lead optimization process both time and cost efficient. Our goal is to automate Free Energy Perturbation calculations to provide access to large scale simulations for lead optimization.


Inna Ermilova

Department of Materials and Environmental Chemistry, Stockholm University

In my last year of the PhD studentship I decided to attend most interesting events in computer assisted drug design. BioExcel 2nd SIG Meeting “Advanced Simulations for Biomolecular Research” in Athens, Greece was one of them. I was even more happy about my choice when my abstract was selected for a poster session because the problem which I was depicting, was related to a hot-topic in pharmacology: drugs against Alzheimer’s disease. Of course, it was nice to present own research but I found it interesting to learn about what other scientists do in the field and what kind of opportunities exist for a future postdoctoral researcher.

Presentations started from an impressive talk by Zoe Cournia about her research and available computational resources in Greece. Later on we found out about new softwares for virtual reality (VR) presented by Marc Baaden. We also got gifts from organizers in the form of VR glasses which we could apply on our cell-phones and try them with BioExcel app. This app could be used even by people who were not from the field and not technically educated. Personally, I would suggest showing it to pupils and bachelor students.This could be inspiring for them and could motivate them to study topics which we were discussing at the workshop. Moving further, we had interesting presentations by industrial representatives regarding challenges which they are facing as well as information about job opportunities.

The amount of information which we received as participants, the opportunities to communicate with people from the field and share experiences with them made me feel that such a workshop shall at least last for 1.5 days with more presenters.


Alexios Chatzigoulas

Biomedical Research Foundation Academy of Athens

It is a sunny day in Athens during September, and the BioExcel 2nd SIG Meeting: “Advanced Simulations for Biomolecular Research” is near to start. I am selected to present my poster entitled “A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on their Crystal Habit”, and I am excited to show the efforts of my long last year work, but I am also excited to learn about the work of other scientists and expand my knowledge.

The BioExcel 2nd SIG meeting brought together scientists from the field of computational drug design being an excellent occasion for discussion of ideas and dissemination of knowledge. The topics covered many aspects of disseminated advances in rational approaches in drug design and discovery, in order to create new methodologies and strategies to achieve earlier and more precise diagnosis, improved targeted therapies and better therapy monitoring. Thus, it was an opportunity for scientists in the field and especially young researchers to get an update of the current trends in drug design.

I delivered a poster presentation titled “A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on their Crystal Habit”, which is a tool for creating nanoparticles for simulation and can be accessed here. I had the opportunity to present this project to many scientists and through fruitful conversation receive feedback for future work. I also met researchers with common interests, with whom I exchanged ideas and views. Finally, attendance of the oral presentations enabled me to be aware of the advances and innovations that have taken place in the fields of computational methods for drug discovery, computational biology, and many others.

See you again in the 3rd meeting hopefully :D


Joana Dulaj

Biomedical Research Foundation of the Academy of Athens

Getting selected for the BioExcel SIG workshop, held in Athens on September 8 was exciting. I enjoyed and feel proud to present my poster about development of a real time gene database for an Android application. It was a great experience to meet scientists from all over the world presenting their work related to my field and advising me about my thesis. It is the kind of event where you learn, teach, share and exchange the scientific (or not) knowledge in a very friendly atmosphere. Furthermore, I feel proud about the other members of my lab which I belong to watch them to present their work in the flash talks and poster sessions.

In the BioExcel workshop I attended many lectures related to my research, which was very important for better understanding of the methods that I have been using in my thesis. The content of the lectures and courses was very interesting and inspired me to try different approaches to answer some questions about my project. Also there was a VR game which I loved and was very exciting. In that game there was a protein in a 3D environment and you move it around the room of the game.

I really recommend people to attend one of the most amazing and well-organised BioExcel events in order to find new international friends, new collaborations, or in general to enrich your network.


Zacharias Faidon Brotzakis

ETH Zurich

Having been awarded a travel grant for the BioExcel 2nd SIG Meeting “Advanced Simulations for Biomolecular Research” on September 8 2018 allowed for fruitful discussions with state-of-the-art researchers and keen infrastructure developers in the marvellous location of Athens.

The site of the workshop allowed combining sightseeing with science. In particular, visiting the Acropolis museum and walking in the city surrounded by lively people and ancient monuments was super fun as well as absolutely breathtaking.

The workshop itself was particularly interesting combining both basic and applied research scientists as well as code and platform developers, thereby bridging the gap between them. In particular, presentations about automated and user friendly platforms of Molecular Dynamic, Free Energy Perturbation (Cournia team), Coarse Graining (Khalid team) and virtual reality visualization of configurations (Baaden) are very useful for my research.

The main speakers revealed amazing topics of interest covering fields such as cell communication and causes of cancer (Del Peraro, Khalid, Cournia). The talk by Jean-Pierre Changeux was particularly mind blowing unraveling complex ways of cell communication.

In between the main speakers, selected participants gave concise presentations on how to possibly use molecular modelling methods – e.g. coming from the fields of material science-into biology relevant projects such as protein folding. These talks led to stimulating discussions during the poster presentation sessions which widened my horizon in many different directions, from cellular biology to state-of-the-art microscopy techniques.

On a personal note, having performed my doctoral and post-doctoral studies abroad, this workshop allowed me for the first time to present my research in my home country – Greece. I was extremely happy and encouraged to hear about the possibilities for regional infrastructures available for peripheral countries of Europe, since this allows for decentralising knowledge and technology and giving equal possibilities. These are actually amazing news!

Last but not least, during this workshop I was lucky to meet with cool and prominent young researchers with whom I am sure I will meet again in the future. I was pleased to present them my recent work on how enhanced sampling molecular modelling can be used to understand protein-protein interactions, a crucial step for understanding cell communication and signalling.

This workshop has given me new friends and colleagues. I hope BioExcel will keep on connecting researchers from all around the world, and I most willingly look forward to the next meeting.


Andres Felipe Vasquez

Department of Chemical Engineering, Universidad de los Andes

After having been selected for the BioExcel Summer School held at Athens on September 8 2018 at Stavros Niarchos Foundation Cultural Center, I immediately knew that attending this event would be a great experience. Undoubtedly, it was a wonderful opportunity to meet people of all over the world who are working in computational biology from different areas of expertise, including team leaders, post-doctoral fellows and PhD students.

My research interests during my master’s degree studies in Biological Sciences and now during my PhD have been mainly focused on molecular modelling and dynamics, drug discovery and cancer research. As a guest PhD student at Istituto Italiano di Tecnologia (IIT), in the city of Genoa, I was given advice to attend this BioExcel Summer School as an invaluable occasion to learn about cutting-edge technologies being applied on my field, lots of breakthrough research and most important, get into direct contact with the people behind all these wonderful advances. It was an open-mind experience to get acquaintance of both new horizons and ideas in computational biology.

Throughout the entire event, I could discuss and exchange ideas with people from many distinct countries who are working on similar lines of research, what I believe is crucial to facilitate the possibility of establishing future international research initiatives. By attending the conferences and poster sessions I met extraordinary people coming from Greece, Spain, Switzerland, Germany, France, England, and Poland. Interestingly, I could also meet many other researchers, developers or creators of well-known software who are working even on branches different from proteins, namely genes, genomes, proteins, systems, as well as training and data application. From my perspective as a third-year PhD student, I strongly believe that the interdisciplinary nature of this field is an essential feature to solve complex scientific problems and challenges lying ahead of us. Therefore, we all definitively must make an large effort in breaking down conventional barriers between people working in ‘apparently’ distinct topics what, in the long-term, offers attractive possibilities in joint research by taking advantage of the fortitudes of different research groups and their members.

I had the chance to visit the Acropolis but I missed having time to stay a bit more in the city. Athens is an incredible place and a dreamed destination for lovers of history, architecture and art. I really wish to come back in another opportunity to know many other interesting sites of this outstanding cosmopolitan metropolis. Finally, I really recommend people to attend BioExcel events in the future to identify not only new colleagues, but also to build potential inter-institutional collaborations, and to cultivate and enrich your own professional network. I will surely be waiting for my second chance.

Thanks BioExcel!


Rodrigo Alonso Ochoa Deossa

University of Antioquia

The 2nd BioExcel SIG meeting was a wonderful experience for me, especially due to the interesting combination of people from industry and academy. During the meeting, both sides shared their experiences around a similar goal: apply biomolecular simulations and data analysis techniques to improve the prediction and current understanding of molecular systems. This allowed me to understand the impact of projects like BioExcel has in the community, empowering the scientific contributions, for example, in the search of novel molecules with potential therapeutic activities among other applications.

As a PhD student from Medellin, Colombia, having the opportunity to assist and be supported by the BioExcel travel fellowships is priceless for my professional formation. Colombia and Latin America are starting to be more connected with these scientific topics, and because of that, it is important to share our progress as well as interact with people from other regions working in similar issues. In the end, the fruitful collaborations created in meetings like this, can highly impact the solution of real-life problems studied by computational approaches.

An example of this is the research group I belong. I’m part of a Max Planck Tandem Group created in Colombia to study from a biophysical perspective the discovery and design of novel therapeutics, diagnostics and vaccines for Neglected Tropical Diseases. In that manner, the use of computer simulations to understand the interaction between the biological entities on a molecular level is key to rationally advance in this quest. The work I presented assessed a set of computational tools to mutate single amino acids in protein interfaces, which is part of a bigger contribution to design de novo macromolecular entities for therapeutic purposes. In fact, I had the chance to talk and network with people from the pharmaceutical industry that are focused on similar goals, which in the end is one of biggest contributions these kinds of meetings can provide to early career researchers like me, and in general to the scientific community.


Arumay Pal

Weizmann Institute of Science

This was my first experience participating in a BioExcel event where I met researchers of different levels – Masters and Ph.D. students, Postdocs, experienced group leaders from academics as well as senior scientists from the Pharmaceutical industry.  It was a nice and neatly organized one-day meeting of limited participants in a cozy venue. The format was a free-form discussion of ideas and results from different areas of computational biomolecular research such as biomolecular modelling and simulations and computer-aided drug design.

The program also included two important current topics in computational biology research – i) how 3D visualization of biomolecules in virtual reality in interactive fashion can be beneficial to understand their structure and interactions, and ii) how computer-aided drug design can be benefited from ‘Big data analysis’. Both the topics were excellently described by leading scientists which was informative and enjoyable. The 3D visualization of biomolecules in virtual reality was also demonstrated by application kits which I experienced for the first time.

Apart from meeting academic group leaders of my field of interest, I also got acquainted with leading scientists from the industry. The experience will be helpful in my career building. I thank BioExcel and the organizers for providing me this opportunity to attend the meeting and present my research. Will be glad to be in touch and look forward to future BioExcel events.


Ioanna Tremi

National Technical University of Athens

This year’s BioExcel meeting “Advanced Simulations for Biomolecular Research” was held in Athens, Greece as a satellite meeting during ECCB 2018 at Stavros Niarchos Foundation and Eugenides Foundation. It was an opportunity for me to attend this year’s meeting since I live in Athens and the selected location for the meeting was ideal. It also allowed me to meet with other people from around the world, researchers, students and post-doctoral fellows. During my Master thesis I worked both on Molecular Dynamics Simulations and experiments. I studied the effects of the 5-trans isomer of arachidonic acid on model liposomal membranes using both directions. This work was published in the Journal of Membrane Biology and it gave me great pleasure to present this work at this meeting and discuss it with other students and researchers.

The meeting was very well organized and everyone was friendly and approachable. The program offered many different lectures some of which I hadn’t heard before and this made my presence there more interesting. All the presenters were very open in answering questions and discussing issues. Many presentations were food for thought and definitely made me look for more information on my research. One thing that was also fascinating was the VR experience both in the meeting, as well as in the mobile application that was proposed to use after the meeting.

It was a great event and I was really happy that it took place here in Greece. I wish more meetings, summer schools and conferences took place here. I really recommend others to attend the meeting because not only it offers new knowledge especially to young students, but it also gives you the opportunity to speak with academic scientists and industry professionals (Pharmaceutical, Food companies). I look forward to attend this meeting again, learn new things and meet more kind and interesting people.

Thank you BioExcel! Keep up the good science! 😊


Anna Popinako

Research Center of Biotechnology

ECCB-2018 was my first, but not last (I hope) main computational event in Greece. I am very glad and grateful to participate in this event! As of now, I am trying to analyze those wonderful days in Greece. It was very interesting and unusual to find some common features between Ancient Greece and Russia.

As a centre of the arts, learning and philosophy in ancient time, not for nothing Athens is named as the birthplace of science. Thus, it was very symbolically to select Athens as a place for the European Conference on Computational Biology (ECCB 2018). Athens is beautiful in September.

And there were several especially amazing hours during BioExcel 2nd SIG Meeting: “Advanced Simulations for Biomolecular Research”. I have heard the lectures of a great lineup of speakers including a keynote by Jean-Pierre Changeux in such interesting place as New Digital Planetarium. I have read some articles of Jean-Pierre Changeux during my PhD. My first (PhD) project has been dedicated to the structural features and dynamics of eukaryotic ion channels. In this project I have done molecular modeling, molecular dynamics, phylogenetic analysis and structural interpretation of three-dimesional reconstructions of different eukaryotic ion channels, obtained by single particle electron microscopy.

I couldn’t participate in the same event with Jean-Pierre Changeux, when I was a PhD Student. Even the unreal dream comes true due to BioExcel! Many thanks personally to every organizer for newsletters, help, forming a friendly atmosphere and taking care of every detail. Jean-Pierre Changeux pointed on the major conception of new pharmacological agents interacting with modulatory sites in different conformational states of ion channels.

I hope it will be as an application for the production of highly selective medicines and will reduce the number of their side effects in future.

Many thanks to BioExcel for helping researchers all over the world!