Mark’s Soap Box

UCSD is using computing fight diseases with Geometry, and they didn’t even need the stem cells from children or adults. Wonder why we don’t see the Hollywood crowd crowing about this?

How Does It Work

The program looks at the geometry of protein molecules to determine it’s function.

In the atomic-level landscape of proteins, shape determines the all-important function of these molecules of life. For example, when a protein molecule responsible for Parkinson’s binds with the cell membrane, will a new drug candidate interrupt this interaction — preventing disease progression and protecting the patient” It all depends on the precise geometry and energy of the protein structures.

It is called MAPAS [you Ph.D types can try it here].

“It’s extremely important to explore the structural details of the zone where the protein contacts the membrane so that we can understand the molecular mechanisms of disease development,” said Tsigelny. “This knowledge gives crucial guidance in selecting which among many possible compounds are most likely to do well in tests to intervene in such protein-membrane interactions and help treat these diseases.”

The researchers describe the new MAPAS tool in the February 2008 (vol. 5 no. 2) online edition of Nature Methods. In addition to Tsigelny, the other authors, who are all at UCSD, include Yuriy Sharikov, Ross Walker, Jerry Greenberg, Valentina Kouznetsova, Sanjay Nigam, Mark Miller, and Eliezer Masliah.

The traditional approach — I am told — is to crystallize the protein and then X-Ray it. This approach allows you to visualize the protein, but it was difficult to know how the membrane and protein interact. The program is believed to make this much easier, leading to understanding and hopefully success in finding cures.

They are currently using MAPAS to research Alzeiheimers Disease.

Tags: Yuriy Sharikov, Ross Walker, Jerry Greenberg, Valentina Kouznetsova, Sanjay Nigam, Mark Miller, Eliezer Masliah, MAPAS, protein, disease, super computing