by Elena Detta
I was attending a lecture about state-of-the-art computer-aided methods in structural biology at the Swiss Summer School in Medicinal Chemistry (October 2018), when I first realised my interest in in silico approaches to study the 3D organization of protein systems.
After a first visit in November 2018, I set up a collaboration with the Computational Biomedicine Institute in the Forschungszentrum Juelich, where I worked for 3 months over the period from January to June 2019. There, I had the opportunity to receive hands-on training and daily support in the use of advanced computational approaches, with the main aim to explore the molecular structure of ‘my target of interest’, Hepatitis B Virus (HBV) core protein, and to gain a deeper understanding of how it works when it interacts with small molecules.
In silico structural biology approaches to enrich my doctoral research
The secondment provided me with the chance to learn the basics of protein modelling (MODELLER) and Molecular Dynamics Simulation (GROMACS). At the same time, I performed Induced-Fit docking experiments (Maestro Schroedinger Suite) and attended some tutorials about how to use MOE software for drug design.
The direct supervision and the high availability of computational resources and tools certainly contributed to accelerate the learning process. With the major goal of advancing my personal research, I focussed my attention on acquiring knowledge and learning advanced in silico techniques that could be used in the next future either in AiCuris or ICIQ either in general for the VIRO-FLOW project to support and guide the process of drug discovery.
Forschungszentrum Juelich: my experience
Situated in the middle of the Stetternich forest in Juelich, the Forschungszentrum covers an area of 2.2 square km. The 400 phD students among the 5700 stuff members here employed work in a green, inspiring and interdisciplinary environment, where chemistry meets physics, biology, medicine and engineering. Scientific events, workshops and talks take place daily and give the possibility to students and professors to meet, discuss and share ideas.
Here I had the great chance not only to operate on one of the fastest supercomputers in Europe, but also to network with many experts and other PhDs in computational chemistry and biology. In a relatively short frame of time I became familiar with the use of different in silico structural biology approaches and gained a good command of the Maestro Schroedinger Suite. Overall, this experience was a good opportunity to challenge myself, both scientifically and personally, and to prove my skills to quickly adapt to a new setting and to work in a more independent manner.