About

Hi. I’m Patrik Nikolić.

My scientific research and interest involve:

  • drug discovery using computational chemistry with emphasis on high-throughput virtual screening protocols and molecular dynamics simulations
  • drug development
  • translational research

For further information and formal introduction, please download my résumé or follow me on LinkedIn and GitHub.

Scientific Research

Biomolecular Structure and Function Group

In 2013, as a student of medicinal chemistry at University of Rijeka Department of Biotechnology, I started working in Dr. Željko Svedružić’s Biomolecular Structure and Function Group and Group (BioSFGroup) on the development of mechanism-based inhibitors of human DNA methyltransferase Dnmt1. While I have primarily used GROMACS and PyMOL in my research, the group relied heavily on software for both research and teaching and used a number of other packages as well. I obtained my master’s degree in medicinal chemistry in 2015 by defending the thesis titled In silico optimization of the first DNA-independent mechanism-based inhibitors of mammalian DNA methyltransferase Dnmt1. Resulting from this work, BioSFGroup later published the book chapter:

The group also published the journal paper:

RxTx Research

In 2019, after Dr. Vedran Miletić returned from his postdoctoral research in computational biophysics at Heidelberg Institute for Theoretical Studies in Molecular Biomechanics (MBM) group to become a Senior Lecturer at University of Rijeka Department of Informatics, we jointly started RxTx, where I entered as a translational research scientist. Our goal was to advance pharmaceutical drug research by improving the scientific software behind the scenes, most importantly the high-throughput virtual screening engine RxDock. We also started using RDKit for data pre-processing at the same time.

By then, the computational resources became more available, drivers necessary for using those resources more mature, and research topics more complex. Thus, the volume of data comprising research inputs and outputs grew exponentially so we have started to employ end-to-end data science solutions, specifically KNIME for workflow automation and data analysis.

We continued the collaboration with BioSFGroup and gave a conference presentation:

  • Koren, R., Martinović, M., Nikolić, P., Odorčić, I., Ostojić, L., Visentin, D., Vrbnjak, K., Miletić, V. & Svedružić, Ž. M. Supercomputers as microscopes for the 21st century: substrate channeling, epigenetic regulation, and molecular basis of Alzheimer’s disease. in 27HSKIKI Book of Abstracts, Zagreb, Croatia (Croatian Chemical Society, 2021).

Dr. Vedran Miletić and I independently published another paper in collaboration with Dominik Kinkela:

We also opened a number of new collaborations with other groups worldwide.

Group for Applications and Services on Exascale Research Infrastructure

In Q4 2021, Dr. Vedran Miletić was promoted to Assistant Professor at Faculty of Informatics and Digital Technologies, University of Rijeka and formed Group for Applications and Services on Exascale Research Infrastructure (GASERI). I continued the collaboration with GASERI as an external partner.

With the recent advent of artificial intelligence, machine learning, neural networks, and deep learning in computational biochemistry, I became increasingly aware that the methods applied in my previous and current research are just not enough anymore. For example, Greg Landrum, the owner of T5 Informatics and the author of RDKit, has been blogging about machine learning using RDKit already for some years.

My goal is to bring the artificial intelligence methods in computational biochemistry to GASERI in order to stay relevant in the long term and be able to tackle any challenge that is interesting both to industry and academia. However, I am aware that such an endeavor is a full-time proposition and I am looking for a way to commit myself full-time to such a research project.

The list of my thus far scientific publications can be found on Web of Science and Google Scholar.

Career in Life Science Industry

Translational Research at Fidelta

A cornerstone of my career has been the position of scientist at Translational Research and Alliances Department at Fidelta Ltd.. With Fidelta being a pharmaceutical contract research organization (CRO), I had the opportunity to work on projects for a large number of originator pharmaceutical companies. My position was designed as a scientist with a high-level overview of all the projects Fidelta had at the time where I provided support to the project management team in preparing, visualizing, and analyzing data on integrated drug discovery projects.

The experience and knowledge I gained with my mentor Vesna Eraković Haber, MD, PhD, MBA of the pharmaceutical industry as a whole proved to be invaluable. My duties also included setting up, monitoring, and closing collaborations with clinical and academic institutions. The drug development projects were mostly focused in oncology, pulmonology, and gastroenterology fields.

I was also working as a “regular” scientist in a wet lab, mostly working on human tissue samples preparation and handling for further tests (ELISA, flow cytometry, immunohistochemistry, etc.).

An overview of my duties can be summarized as:

  • clinical study site visits including qualification, initiation, monitoring, and close-out visits according to GCP, GDPR, and other relevant national legislation
  • writing of clinical study protocols with accompanying procedures and documents
  • managing communication between Clinical Investigators, clients, local regulatory authorities, and research teams
  • performing in vitro and ex vivo assays for drug development

Sales and Applications Specialist for Life Science at Biomedica dijagnostika

A new step in my career was an opportunity to develop and expand a research portfolio of AddLife Group. I started working for Croatian subsidiary Biomedica dijagnostika Ltd. of Biomedica Group as a Sales and Application Specialist for Life Science portfolio. The main reason I took up this opportunity was a challenge to introduce new and cutting-edge technology in the competitive European market.

To be fair, nobody expected global pandemics of this size and scope, and certainly not the size and scope of the disruption it caused on global manufacturing and distribution chains. Furthermore, nobody expected industry-wide changes in the way the business is being done. All those changes made that challenge and the goals I set myself even harder to achieve. Given my previous experience and know-how coupled with the forward-looking team at Biomedica and AddLife, I’m happy to say that I achieved those goals and then some.

Similar to the position at Fidelta, both the portfolio I’m working in is diverse and includes a large number of manufacturers, and the clients I’m working with range from small academic groups across public and private hospitals to pharmaceutical companies. A wide overview of industry trends, setting up commercial contracts, and following up on successful sales projects is the most valuable experience I could hope to gain in this industry. That was one of the goals I set myself up back when I was joining Biomedica, as well.

An overview of my duties can be summarized as:

  • regular meetings with scientists, physicians, nurses, and other support members in the pharmaceutical industry, academia, public hospital systems, and private hospitals
  • participation in and organization of congresses
  • product demonstration and performing demonstrations for a selected portfolio