Nimbus researchers think that part of the reason is that most tools fail to incorporate the thermodynamics of the resident water molecules in the protein's binding site. "The need for improved water models is a widely acknowledged yet seldom-addressed limitation of current methods," says Christopher Snow, a postdoctoral researcher at Caltech who is not involved with the company. It's difficult to model the energy of water molecules.The company's work over the past year has been to use its software to sift through a list of 1,200 potential drug targets to a final 20 that show that most promise. Work will focus on targets involved in inflammation, oncology, metabolic disease, and antibiotics, according to the report. You can read the full article here.
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July 19th, 2011
Will computational modeling revolutionize drug discovery? Apparently Bill Gates, who has invested in a startup focusing on computational chemistry, thinks so. Computational modeling has crept slowly into the world of pharmaceuticals over the last two decades, but while it's currently used by many companies, it generally remains a small component of drug discovery. Cambridge, MA-based startup Nimbus Discovery hopes to move it to center stage, according to a report this morning in MIT's Technology Review. Nimbus Discovery is the result of a partnership between Schrödinger, the maker of computational drug discovery software that is already widely used in the pharmaceutical industry, and venture capital firm Atlas Venture. One of the stumbling blocks in current computational work has to do with the modeling of how water molecules in various proteins react. Targeting this current weakness, the startup is taking the following approach: