"Game changer": a new technology that simulates molecular life with computers

The University of Kansas published a landmark report in this week's Proceedings of the National Academy of Sciences proposing a new technique

According to first author Ilya Vakser, director of the Computational Biology Program and Center for Computational Biology and professor of molecular biology sciences at the University of Kansas, the study of computer modeling of life processes is an important step

Vakser said: "It is tens of thousands or hundreds of thousands of times

Until now, a major obstacle to modeling cells by computer is how to approach proteins located at the core of cellular processes and their interactions

According to investigators, both methods have advantages and disadvantages

"Our proof-of-concept study connects two modeling approaches to develop a method

Vakser's co-author is Sergei Grudinin of the Alpes University of Grenoble, France; Eric Deeds at UCLA; University of Kansas PhD student Nathan Jenkins and University of Kansas Computational Biology Program Assistant Research Professor Petras Kundrotas

After conceptualizing how best to combine the benefits of the two protein modeling methods, the team developed and wrote an algorithm to drive the new simulations

Vakser said: "The most difficult challenge is to develop algorithms

But once they make a breakthrough, they can start validating the

Vakser said: "The pattern is simple, very clear

But Vakser says that until his team publishes the new paper, the approach has not yet been applied to the kinetics of protein interactions in the cellular environment, which is the focus of

"Because there are so many fewer high-probability states than low-probability states, Vakser says, this gives us a huge increase in computational speed—tens of thousands to hundreds of thousands of times

The University of Kansas researcher says his cell simulation method could be used to study human health and treat disease

Vakser said: "This method can be used to study molecular pathways

Vakser said the new simulation technology offers many promising avenues

"This includes applying this approach to proteins interacting with nucleic acids, RNA and DNA
," he said.
"In addition, we wanted to explain the flexibility of molecular shape, correlate it with the rapidly evolving experimental study spectra of the cellular environment, and apply this process to a model of an actual cell – its actual molecular components clustered together
.
"

Journal Reference:

1. Ilya A.
   Vakser, Sergei Grudinin, Nathan W.
   Jenkins, Petras J.
   Kundrotas, Eric J.
   Deeds.
   Docking-based long timescale simulation of cell-size protein systems at atomic resolution.
   Proceedings of the National Academy of Sciences, 2022; 119 (41) DOI: 10.
   1073/pnas.
   2210249119