Molecular dynamics simulations represent an increasingly important cornerstone of modern scientific research, thanks to their unparalleled ability to meticulously describe fundamental aspects of complex systems. It is not a coincidence that nowadays molecular simulations are considered a "virtual microscope" from which admire and examine biological processes, as well as confirm through "computational assays" innovative hypotheses which provide the basis for designing new experiments. This was made possible by the continuous efforts in developing more efficient algorithms and the exponential growth of computing power. Prof. Vittorio Limongelli and Prof. Michele Parrinello of the Institute of Computational Science (ICS) at USI, together with other colleagues, members of the Plumed consortium, recently published on Nature Methods "PLUMED-NEST" ( www.nature.com/articles/s41592-019-0506-8 ), the first public repository that allows free access to protocols and models of these "assays" at virtual microscope.
This project is based on a technology originally developed at USI that is now spread worldwide. PLUMED-NEST gives the opportunity to learn new computational methods and protocols developed in the field of enhanced sampling molecular dynamics simulations. Users not only have access to algorithms, but they are also able to download input files and data necessary to reproduce the results published on peer-reviewed, high-impact international scientific journals of chemistry, physics, material science and biology. The group of Prof. Limongelli contributed by spawning in PLUMED-NEST the protocol of the "Funnel-Metadynamics", an original technique designed to study the molecular recognition of a drug with its molecular target, and the "Coarse-Grained MetaDynamics", a method employed to study interaction between proteins in their biological environment.
According to Prof. Vittorio Limongelli, "PLUMED-NEST" represents a paradigm shift with an important message to the scientific community, that is transparency and knowledge sharing are two essential conditions to promote progress. "PLUMED-NEST" will impact research in molecular simulations, further accelerating the development and the diffusion of computational techniques in the short and especially in the middle/long run.
A valuable research and a role in the international landscape
The contribution to the birth of "PLUMED-NEST" upholds the value of scientific research that USI has carried on for years in the field of simulations applied to natural and life sciences. A further evidence of the central role played by USI, especially by its Institute of Computational Science, is given by the organization of the first edition of the BImBS school "BioInformatics meets BioSimulations in protein and DNA studies: from theory to practice", which was hosted at USI from the 5th to th 12th of October.
At BImBS world-class experts in the field of bioinformatics and bio-simulations seated for the first time together to discuss interdisciplinary research projects and train young scientists, with focus on proteins and DNA studies.
BImBS school has been supported by CECAM, Novartis, Hasler Stiftung and other actors in the field of life sciences and it has been organized by Prof. Vittorio Limongelli (Faculty of Biomedical Sciences and Institute of Computational Science), Prof. Daniele Di Marino (University of Ancona) and Prof. Francesco S. Di Leva (University of Naples).