IPPT PAS Scientists Publish in „Nature Communications”

A research team led by Dr. hab. Adolfo Poma Bernaola from the Institute of Fundamental Technological Research of the Polish Academy of Sciences (IPPT PAS) has reached a significant milestone with the publication of their latest work in Nature Communications. The study introduces GōMartini 3, an advanced biomolecular simulation method designed to deepen our understanding of complex biological systems.

“This work represents more than seven years of development,” says Dr. Poma. “I began designing the original GōMartini approach with the vision of creating a flexible and efficient method for studying biomolecules at large scales. Now, with GōMartini 3, we have taken a major step forward in realizing that vision.”

Redefining Biomolecular Simulations

The newly developed GōMartini 3 builds on Dr. Poma’s original GōMartini model, first introduced in 2017. This computational approach enhances the widely adopted Martini 3 force field, allowing researchers to investigate biological processes with remarkable precision. With improved capabilities for simulating protein–membrane interactions, protein folding mechanics, and intrinsically disordered proteins, GōMartini 3 opens new avenues for research in areas such as cancer biology, neurodegenerative diseases, and molecular biotechnology.

“The ability to simulate complex biological systems at larger time and length scales is essential,” explains Dr. Poma. “We can now model processes that were previously impossible to capture using conventional simulation techniques. This brings us closer to bridging the gap between computational biology and real-world molecular behavior.”

A Competitive Edge in Computational Biology

In the fast-evolving field of biomolecular modeling, several approaches—such as SIRAH, UNRES, and SPICA—have gained prominence. However, Dr. Poma emphasizes that GōMartini 3 stands out due to its unique combination of flexibility and accuracy.

“One of the strengths of GōMartini 3 is its versatility,” he notes. “Unlike many other models, it is not restricted to a single type of biomolecule. It enables us to study proteins, lipids, and nucleic acids simultaneously, making it a powerful tool across a wide range of research disciplines.”

The Martini 3 community, renowned for its rigorous validation processes and collaborative ethos, has played a vital role in advancing biomolecular simulation. Notably, Martini 3 was instrumental in achieving the first whole-cell simulations—an accomplishment that brings science closer to replicating cellular environments with unprecedented accuracy.

International Collaboration at the Heart of Innovation

The development of GōMartini 3 was made possible through extensive international collaboration, involving scientists from Poland, France, the Netherlands, Germany, Spain, Brazil, Portugal, Chile, and South Korea. The project was led by leading figures in the Martini 3 initiative, including Dr. Paulo C.T. Souza, Dr. Sebastian Thallmair, and Prof. Siewert J. Marrink.

“Science knows no borders,” says Dr. Poma. “This project demonstrates what can be accomplished when researchers from different backgrounds and countries unite to tackle complex challenges. The synergy between experimentalists and computational scientists was crucial in bringing GōMartini 3 to life.”

With its ability to capture molecular behavior at a new level of detail, GōMartini 3 is poised to redefine the standards of biomolecular simulations and deliver new insights into some of the most urgent biomedical challenges of our time.

“I am excited to see how the scientific community will adopt this method,” concludes Dr. Poma. “Our aim was to create a tool that not only advances research but also inspires new ideas and discoveries in molecular biology and biophysics.”

Scientific publication

Souza, P. C. T., … Poma, B. A., & Thallmair, S., GōMartini 3: From large conformational changes in proteins to environmental bias corrections. Nature Communications, 16, 4051 (2025). DOI: 10.1038/s41467-025-58719-0