BioSolveIT Scientific Breakthrough in Predicting Binding Affinities
Published: Apr 04, 2011
Ever since the 80s when the first computer methods emerged, computer predictions of the strength of binding of small molecules in a protein cavity have so far largely failed, even when employing enormously long compute times. Professor Matthias Rarey from the Center for Bioinformatics (ZBH) at the University of Hamburg, consortium member and world renowned expert in the field says: “When we first started this research project almost seven years ago, scientists all over the world were already engaged in the quest for improved scoring functions for more than a decade. It was clear to me that that we had to devise completely new ways to approach this problem. At that time, the key idea for HYDE was introduced to me by Dr. Gudrun Lange and colleagues at Bayer CropScience. Dr. Lange suggested a hitherto unknown, unified description of the most important driving forces to complex formation. This was the basis on which the consortium started to develop HYDE”.
BioSolveIT’s premium docking suite FlexX, an industry standard for structure-based design, served as the basis of the HYDE implementation. After mastering dozens of seemingly insurmountable hurdles along the way, the development partners ZBH, Bayer CropScience (ISIN DE0005752000 / WKN 575200), and BioSolveIT finally mastered the consistent description of hydrogen bonding, the hydrophobic effect, and desolvation using a single, concise formula.
Early drug discovery applications of HYDE have been reported as being extremely successful. Dr. Lange presented at the ICCS conference in 2008 hit rates of up to 70% in real-life projects. At this year’s National ACS Meeting in Anaheim, CA, the successful application of HYDE on several benchmark data sets was reported. FlexX/Hyde ranks among the top-tier computer programs and outperforms the competition on many targets.
“However, more important than any comparison of numbers can ever reveal, HYDE exposes issues with a given lead molecule graphically. It can identify deficiencies and highlights where there is room for improvement. HYDE guides researchers towards new routes for compound optimization by its intuitive, colored visualization: “Green atoms give good scoring contributions, red ones are unfavorable”, Dr. Lemmen, CEO of BioSolveIT, explains. “Based on this analysis medicinal chemists will immediately come up with ideas of how to modify a compound for improved binding affinity. We are proud to be part of the team that arrived at what can be considered no less than a breakthrough for predicting binding affinities”.
HYDE was released just last Thursday to the general public and presented at the ACS National Meeting in Anaheim, California.
BioSolveIT GmbH (www.biosolveit.de) is a Bio- and Cheminformatics company. Its core businesses are software, services, and research collaborations. With three founders in academia, BioSolveIT has its backbone in science and catalyzes the genesis of products off of basic research successes. The company’s software products are world-renowned such as the molecular docking software FlexX and reach a significant customer base. With the FTrees program BioSolveIT took leadership in ultra-fast virtual high throughput screening using a fragment-reassembly based approach. User-friendly GUIs and a suite of fragment based design tools complete BioSolveIT’s current software offerings.
Dr. Marcus Gastreich
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