I recently submitted my thesis, and while completing a PhD thesis is a significant milestone, the submission process can be quite overwhelming due to various administrative requirements. To help fellow PhD students navigate this often-overlooked aspect of their journey, here are some practical tips:

1. Understand Requirements: Familiarize yourself with your university's guidelines for thesis formatting and submission. Each institution has specific rules you need to follow, including downloadable templates.

2. Plan Your Story: Embed your research in a coherent narrative. Draft a plan and identify any gaps, especially in the results section, to determine which remaining experiments need to be completed.

3. Start Early with Administrative Tasks: Begin collecting the necessary documents and signatures well in advance of your submission deadline. Keep in mind that people may be sick, on holiday, or busy with other commitments. In Germany, I had to submit additional documents such as certified copies of my diplomas and letters to the dean and the university —none of which could be digitalized. This required extra printing time!

4. Organize Your Documents: Save all thesis-related materials on a drive, including drafts, feedback, and administrative forms, to avoid last-minute scrambling.

5. Seek Support: Don’t hesitate to reach out to your committee, peers, or administrative staff if you have questions or need clarification about the submission process. They are familiar with the requirements and can provide valuable insights.
​
Good luck to all PhD candidates! 

​My ~150 pages of cumulative thesis along with 50+ printed documents required for the submission

Check the blog post by ESR12 ​Léxane Fournier

As Stockholm prepares to host the Nobel week this coming December, the rest of the world is still discussing the recently awarded Nobel prizes in chemistry and physics. This year's awards have sparked intense debate, as they highlight the growing influence of artificial intelligence (AI) in scientific research. The recognition of AI-driven discoveries in both chemistry and physics has raised questions about the future of scientific inquiry and the role of technology in advancing our understanding of the natural world.

The 2024 Nobel Prize in Chemistry was awarded jointly to David Baker, Demis Hassabis, and John Jumper for their groundbreaking work in protein structure prediction and design. Baker was recognized for his achievements in computational protein design, while Hassabis and Jumper were honored for their development of AlphaFold2, an AI model that can accurately predict protein structures. The influence of AlphaFold reaches far beyond academia; it has made protein structure predictions widely accessible through the AlphaFold Protein Structure Database, which now boasts over 214 million predicted structures. As ALLODD is a drug discovery-focused consortium, these AlphaFold predictions are particularly valuable for our research, potentially accelerating the identification of novel drug targets and the design of more effective therapeutics.

In an unexpected turn, the Nobel Prize in Physics was awarded to John J. Hopfield and Geoffrey Hinton for their seminal contributions to the foundational methods that enabled the development of machine learning. Hinton, often referred to as the "Godfather of AI," was recognized for his pioneering work in artificial neural networks. This decision has sparked discussions about the boundaries between traditional scientific disciplines and the emerging field of AI.
​
The recognition of AI-driven research in both chemistry and physics has elicited mixed reactions from the scientific community. Some researchers have questioned whether these awards align with the traditional scope of these disciplines. However, others argue that these awards reflect the transformative impact of AI on scientific research. As we reflect on these awards, it's clear that AI is reshaping the landscape of scientific discovery. While some may debate the timing of these recognitions, there's no denying the profound impact that AI-driven research is having across multiple disciplines.

P.S. If you ever are in Stockholm in the first week of December, make sure to make the most of the Nobel week events!
- Go visit the lectures by the newly awarded laureates at Karolinska, Stockholm University, and KTH.
- Enjoy the light illuminations dedicated to past Nobel Prize awards scattered throughout the city! Check out the program here: Nobel Week Lights – Stockholm | 2024; the lights on Stadshuset are usually the most impressive.
- Don't skip the Nobel Prize Museum; even if you're a science geek, it can surprise you with some secret facts about the laureates.

 Image credit: Nobel Week Lights 2024 - Visit Stockholm

​Last month, I had the amazing opportunity to return not only to Barcelona but more specifically my hometown neighbourhood, where I attended the EuroQSAR 2024 conference.

The event covered a wide range of topics within the Drug Discovery field, including advancements in AI and machine learning for QSAR modelling, 3D-QSAR techniques, molecular dynamics simulations, and cheminformatics integration. The conference also explored emerging technologies like multi-omics integration, ligand-based virtual screening, and the ethical implications of AI in drug discovery, alongside workshops and discussions on practical applications, data transparency, and interdisciplinary collaboration.

During that week, I had the opportunity to present my research to my peers in a poster session, where I received very interesting feedback from colleagues and members of my former research group who were also attending the event.
Of course, no conference would be complete without a gala dinner, and we were taken all the way up to Tibidabo mountain, to the Observatori Fabra.

We enjoyed a lovely dinner with the best possible view of Barcelona, followed by a guided visit to the observatory. To culminate the night, we had the chance to observe Saturn through the 120-year-old telescope and take in a 360-degree view of the city as we walked around the dome.
​
I felt extremely lucky to be back home and enjoy my city while also enjoying the best science.

Hi everyone! It's time for my ALLODD blogpost :)

This past July and August, I had the exciting opportunity to work at Forschungszentrum Jülich (FZJ) as part of my secondment with ALLODD.

During my time there, I focused on QM/MM simulations of the glycine receptor to better characterise cation-pi interactions, a key element in understanding receptor behaviour and function.

Secondments are invaluable training tools, especially for PhD students. In this blog post, I will highlight their importance.

In many PhD programs, and especially ITNs, ESRs have the chance to get trained through secondments which according to the definition are a „detachment of a person from their regular organization for a temporary assignment elsewhere”.  Secondments essentially represent a period spent abroad working in a different workplace (labs in our cases), focusing on a specific project. We could thus say that metaphorically speaking, they represent the equivalent of a mission for us for scientific growth improvement. But what do exactly secondments mean to us? And why can they be so important?

Like other forms of detachments, surely a contributing role is played by the push they provide in getting out of our comfort zones and routines, adapting to new environments and scientific approaches, and settings. However, they primarily represent a tool for broader expertise development and training. 

 These periods abroad allow us to work in different labs, focusing on specific projects that may be related to or detach from our primary research. The goal is to develop aspects of the project that we are either unable to explore in our usual settings, can only explore partially, or that may require the integration of different approaches. These experiences are thus invaluable for gaining new perspectives on research problems.

Additionally, these exchanges allow us to take advantage of local equipment and environments, providing flexibility and experience with similar software and tools, or even the opportunity to use new ones, which is also important.  Upon returning, we can merge and enhance the knowledge gained with our primary lab's expertise. In addition, they often allow us to dive into different research fields and learn or get a glimpse at the deeper and complex variegations of research allowing us to get a deeper understanding of the challenges to face. They may also allow us to address what we are facing in our field with a more informed perspective.

Personally, in fact, I have found these tools very insightful and useful. As a synthetic chemist, I often notice the tendency to think of molecules and chemical modifications in a somewhat more simplistic or "plain" manner, while the computational approaches explored in some of my secondments have allowed me to recognize the deeper complexity of the drug optimization and to understand that the process should never be reduced to a simple, two-dimensional view.

To sum up, my secondments have allowed me hands-on experience with computational software used in drug discovery, exposed me to different mindsets and approaches and even joined engaging scientific discussions which would have been less likely to happen! Secondments offer not only the chance to learn new techniques but also the opportunity to engage with diverse scientific mindsets and approaches. This opens up the possibility of meaningful collaborations that might not be possible or would happen differently if I had stayed in my home country.

These are just some of the many benefits: meeting other experts, hearing personal stories, and seeing how different paths and minds intersect, I do believe this fosters networking, and contributes to a shared European identity. The different approaches to the projects, meetings, interpretation of data and scientific papers, and software, even when using the same software or working on similar tasks, are intriguing and open-minding.

Therefore, I would define these scientific tools as essential allowing a better exchange, as they facilitate exchange. After all, isn’t scientific progress built on the exchange of ideas and discoveries (and thus minds)?

So that’s how I would spell/summarise them out as: 
Scientific
Enriching
Correspondences
On
Novel
Data-exploration
Matching
Engaging
Networking
Team-building
Strategies
 
Thank you, ALLODD and the European Commission, for supporting this!
Regards,
ESR7 Vincenzo Di Lorenzo

Summertime is usually the time of the year when things slow down, and the lab gets a bit quieter. A good time to catch up on reading all those scientific papers that accumulate throughout the year in my “to read” bookmark folder or as a pile of printouts on my desk. With the summer (at least in Berlin) coming to a close, this is a good occasion to reflect on practices of how to keep up with scientific literature – a topic haunting me at times given the almost infinite and ever-increasing number of interesting papers out there.

For me personally, scientific papers fall into two categories. Category 1 includes scientific papers that are directly related to my field. These are publications dealing with “my” target protein, or reporting synthesis procedures that I want to apply. The second category more broadly entails reviews, perspectives and case studies unrelated to my daily work. While I usually make time to read “category 1 papers” as soon as possible the latter ones accumulate in my web browser and on my desk.

Let’s first reflect on how to find relevant scientific papers. Probably the most obvious are field-specific scientific journals. Through a subscription to their article alerts, you’ll receive regular updates on new research published. A second strategy that I find useful is to use citation tracking for seminal papers, e.g. in Google Scholar. It allows you to discover the latest research building on these groundbreaking articles and thereby stay up to date on a research topic. Finally, I often find inspiration for readings in online discussion groups and blog posts. These channels have the advantage that they provide, apart from the references themselves, other researcher’s opinions, criticisms and ideas on the respective publications in the form of comments. Translated into the real world, journal clubs are a great opportunity to uncover new literature as well, and discuss it with peers of course.

Once the sources for relevant literature are established, we should turn to a more critical aspect: How to make time to browse and read scientific literature. One strategy to maintain a steady reading pace is to set aside dedicated time for reading. While this may work for some people, I never managed to uphold such a routine. Rather I try to use regular “downtime” for reading, e.g. during waiting time in the lab or commutes.

Finally, let’s review strategies for efficient reading and note-taking. During one of our early ALLODD workshops, I learned the following approach to scientific reading that I have since adopted: Starting from the abstract, I continue by reading the conclusions section of a paper. This helps me to decide whether the paper is worth a deeper read. If it is, I either focus on the figures and tables to identify paragraphs that hold the information that I am looking for, or I continue reading the entire piece from introduction to end. While reading, I like taking notes. I use colour-coding to highlight text and categorize my notes into “hypotheses”, “key findings”, “open questions”, etc. I also find it useful to summarize key points right next to a paper’s title. You may also want to highlight critical data, e.g. the potency of a reference compound that you may want to refer back to later. Likewise, some citation managers allow the addition of keywords or notes to imported publications, which can help retrieve studies at a later point in time. When your goal is comprehensive literature research on a given topic, you may want to compile your notes alongside screenshots and schemes into a larger document that summarizes the findings. 

In summary, keeping up with the literature next to daily lab work and writing a PhD thesis is a continuous and at times challenging task. Setting up article alerts, using citation tracking as well as leveraging social media helps to discover relevant publications. Whether you decide on a dedicated time for reading or squeeze it in during downtime in the lab, efficient reading and annotation strategies alongside citation programs help to manage the sometimes daunting amount of information.
​
Do you have any strategies to find, read and annotate scientific literature? Feel free to share them in the comments section!

In October 2023, I had the wonderful opportunity to complete a two-month secondment at the CAMD (Computer Assisted Drug Design) lab in Urbino, Italy, under the supervision of Prof Giovanni Bottegoni. As a purely experimental biochemist, this was my first foray into an actual computational lab and I found the experience very enlightening. Of course, I had had previous introductions to computational methods and case studies from some of my Biochemistry courses, as well as from presentations at various conferences, and not the least from my fellow ESRs hailing from the computational side of the allostery field. However, in this case, I found the adage “experience is the best teacher” to be true. My hands-on use of tools such as Schrödinger and VMD showed me in a concrete way what it must be like to be a computational scientist, and I now have a better understanding of the typical workflow, as well as of the stakes of such work, including the balance between making faster versus more detailed simulations. Additionally, although my own training focused on proteins I was already familiar with from my experimental projects (the melanocortin receptors), several of my colleagues in Urbino were starting various new projects on completely different targets. This contrasts greatly with how experimental labs usually function with the focus remaining largely on related and/or functionally similar proteins across most projects. Despite this, at the CAMD lab, we could still help each other out, which fostered a real sense of camaraderie and a greater understanding of each other’s goals. I believe, now more than ever, that the future of science, and drug discovery in particular, truly relies on, not just one or the other, but the symbiosis of both computational and experimental methods. Thus, it is crucial to understand the possibilities as well as the limits of both, in order to lead to optimal collaborations.

Finally, I would like to highlight the backdrop of my journey into the computational world: the gorgeous city of Urbino, relatively unknown internationally, but a marvel of Renaissance arts and architecture, as anyone attending the recent ALLODD conference there surely noticed. I was happy to return once more and have the chance to say a quick hello to my former colleagues at the CAMD lab. 

More than two years have passed since I joined ALLODD and I am now delving into scientific conferences with one objective: share. Conferences are great opportunities to meet with people from your field and I was really amazed by the kindness of people who are always happy to discuss scientific ideas but also share their thoughts on career path. Among numerous insights, here are the most significant tips:

Be curious
As scientists, we enjoy uncovering new problems and devising innovative solutions. Cultivating a curious mindset involves continuous learning and staying connected with the latest advancements in your field and beyond. Embracing curiosity fuels your drive to seek out new challenges and opportunities with happiness.

Be focused
Establish clear career goals and remain resolute in your pursuit of them. A focused approach ensures that you stay on track and work diligently towards achieving your ambitions. By staying unwaveringly focused, you can navigate through the complexities of your scientific journey with purpose and determination.

Build a network
Whether your professional aspirations lead you towards academic pursuits or the industry, the value of building a strong network cannot be overstated. By fostering a network, you can create a supportive ecosystem that is vital for support, guidance, and opportunities. Funnily, I met at these conferences people who worked in Darmstadt, Germany (where I am currently living) or even in Clermont-Ferrand, France (where I studied). In France, we have a saying “Le monde est petit” (the world is small).
​
Be unique
Last but not least. Each scientific journey is inherently distinct, shaped by individual experiences and perspectives. Embracing your unique attributes and experiences is a powerful way to differentiate yourself and pique the interest of others. By showcasing your uniqueness, you can carve out a compelling narrative that sets you apart in the scientific community 

​On 27th February- 1st March 2024 we ESRs had the great chance to get trained through the 3rd ALLODD Training School in the J&J campus in Beerse, Belgium “IPR Training for Researchers & ESR Presentations on the Progress of their Research”. 

It was a great opportunity to get in touch with the industrial world once again and experience also the personal stories of some of the speakers alongside training and information. It has been very interesting to get to know how the “big pharma” is trying to support innovation through several partnerships and founding even physical ones like the JLABS and get in line with the new guidelines like the project for the reduction of emission which Johnson will try to reach in 2026. Having a geothermal power plant within a campus is surely quite impressive!

Also, the attention to animal health care, it’s something I am sure people are expecting to see more and more applied and this is also a great achievement. Because if it is true that (unfortunately I would say!) they are still required, it is also true that our efforts can be applied even more in this sense, after all (trying to relieve pain isn’t what we should be trying to focus on?) I just hope we will see more and more of this in future and worldwide!

Alongside this, we had the opportunity to get in touch with very interesting talks like intellectual property and Project management and partnerships on the first day and scientific ones on Car-T cells therapy, PROTACs and the kinases. In sum a well-compelled series of talks ranging from biology to chemistry, medicinal chemistry and more! 

But this was not all, on the third day we had to practice (and I would dare to say re-learn!) how to introduce ourselves rapidly but exhaustively in a 4 and then in 1-minute pitches trying to catch as much as possible, which is surely not an easy task! Yet it is interesting to get a little detached from our daily way of expressing ourselves within the scientific community and get more to the general public. After all, as George Orwell has greatly shown in 1984 behind simplification there can be a huge work, but I would add sometimes this can also be very beneficial! 

All this simplification process is in fact one of the basic sets for effective communication in which a key role is also relying on intonations, gestures, and looks and is always very important to keep in mind!
​
We cannot be thankful enough to ALLODD and Janssen Pharmaceutical for this experience and further opportunity and as learned from hearing the story of Janssen himself, proceed even with more enthusiasm cause the clock is ticking and “patients are waiting”. And after all, we are scientists, and we hope to give our contribution also to help!