clock menu more-arrow no yes

Filed under:

Google PageRank algorithm used in tool to model interactions between molecules

New, 9 comments

Associate chemistry professor Aurora Clark of Washington State University and colleagues Barbara Logan Mooney and L. Rene Corrales have applied Google's PageRank algorithm for determining the relevancy of links to chemistry to help model the interactions between water molecules. It's called moleculaRnetworks, and it looks at how many hydrogen bonds each water molecule has and how many bonds neighboring molecules have to create its computational model.

Hydrogen Bonding H2O water
Hydrogen Bonding H2O water

Can two seemingly disparate things — Google's PageRank and hydrogen bonding in water — come together to create a tool that can help predict and map out the interactions between millions of molecules? It might sound far-fetched, but associate chemistry professor Aurora Clark of Washington State University and colleagues Barbara Logan Mooney and L. Rene Corrales have done just that and explained it in a paper published in the Journal of Computational Chemistry. It's called moleculaRnetworks, but before we get into just what it does, let's clear up some of those terms: PageRank is a patented algorithm that helps Google determine the relevancy of links, and hydrogen bonds (seen above) are relatively strong forces that attract molecules like water to each other.

Unlike PageRank, which ranks a result based on how many times it has been linked to by other sites (and how popular each of those sites are), moleculaRnetworks ranks water molecules by how many hydrogen bonds it makes and how many of those bonds each of its neighboring molecules have. How does this help in chemistry? Well, in a solution like water with table salt dissolved in it, the software creates computer models that show how the water molecules and the dissolved salt arrange themselves and how long they'll remain in those orientations.

According to the paper, this can be used to help predict reactions and carry out research without the need for costly lab experiments and does so more universally and easily than other tools. Associate professor Aurora Clark says the software could ultimately be used to create drugs and investigate how misfolded proteins lead to diseases. While Clark and her team focused on water-based solutions, they say that with some simple modifications the system could be used with others as well — even those that don't exhibit hydrogen bonding. As with most research we'll have to wait and see what precise advancements it'll bring, but for now it's at the very least an intriguing meeting between the worlds of the internet and the natural sciences.