Question

I am fairly new to the field of oarse-grained molecular systems. I am aware that there are a lot of different already developed CG algorithms. Since there are so many, I struggle to find what I'm looking for. I wonder if there is a CG algorithms that simplifies a molecule drastically, for example a method that describes a mAb with around 20k atoms with only 12 or 20 beads while not assuming the number of beads beforehand, but rather choosing a partitioning that is most favorable according to a certain metric. Is any such method developed and also open-source?

Answer 1

Yes, the Martini force-field is a CG algorithm that can drastically simplify molecules by dividing them into large groups of beads. The number of beads used is determined based on favorable partitioning, and it has been successfully applied to model monoclonal antibodies with thousands of atoms.

Step-by-step explanation:

Yes, there are coarse-grained (CG) algorithms that can simplify a molecule drastically. One example of such an algorithm is the Martini force-field, which is widely used for modeling CG molecular systems.

The Martini force-field divides the molecule into large groups of atoms called pseudo-atoms or beads, which represent the coarse-grained particles.

The number of beads used to represent a molecule is not predetermined but rather determined based on the favorable partitioning according to a certain metric.

The Martini force-field is open-source and has been successfully applied to describe various biological molecules, including monoclonal antibodies (mAbs) with thousands of atoms.