OpenEye Launches The 'SAMPL' Blind Challenge

Main Category: Eye Health / Blindness
Article Date: 28 Jan 2008 - 1:00 PDT

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OpenEye Scientific Software, Inc., developer of innovative molecular modeling and cheminformatics solutions for drug discovery, announced the launch of the first edition of the Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL-1) blind challenge.

SAMPL is a blind test of protein and ligand modeling; an analysis of methods on data not seen by participants. "With SAMPL we intend to avoid 'who won, who lost'," explained Dr. Anthony Nicholls, President and CEO of OpenEye Scientific Software. "Rather, we see this as an opportunity for groups to test their methods, learn from the experience and share lessons learned." In addition, third party testers, particularly professional modelers, are encouraged to participate so as to allow comparisons of single methods when used by several, independent, participants.

SAMPL-1 will consist of two sets of protein-ligand binding data, generously provided by Abbott Labs and Vertex Pharmaceuticals, and sixty-three vacuum-water transfer energies, courtesy of Peter Guthrie at the University of Western Ontario, and Chemical Computing Group. The two sets of protein-ligand data each have between twenty and seventy active compounds, the majority with protein-ligand crystal structures. The assessment will consist of three parts:

1. Virtual Screening.
2. Predicting binding poses.
3. Predicting binding affinities.

"Hopefully SAMPL will prove useful and become a regular event. There are many possible variants we could try in future assessments, such as providing partial information, e.g. a subset of actives or binding modes, more typical of an industrial project setting. Additional physical properties, such as tautomer ratios, pKas, and thermodynamic data could be sought. I strongly believe a prospective component to our field will help us judge progress and I hope many modelers both agree and contribute," concluded Dr. Nicholls.

The results of SAMPL-1 will be presented at the CUP IX meeting, March 17th-19th in Santa Fe. All participants will be offered a speaking slot at the meeting. The deadline for submission of results is on February 18th, 2008, one month before the CUP IX meeting. For more details, please see http://sampl.eyesopen.com/.

About OpenEye

OpenEye Scientific Software Inc. is a privately held company headquartered in Santa Fe, New Mexico, with offices in Boston, Massachusetts and Strasbourg, France. It was founded in 1997 to develop large-scale modeling applications and toolkits. Primarily aimed towards drug discovery and design, areas of application include chemical informatics, structure generation, docking, shape comparison, charge & electrostatics and visualization. The software is designed for scientific rigor, as well as speed, scalability and platform independence. OpenEye makes most of its technology available as toolkits - programming libraries suitable for custom development. OpenEye software typically is distributable across multiple processors, supports 64-bit processing, and runs on Linux, Windows and Mac OS X, as well as HP, IBM, SGI and SUN flavors of UNIX.

http://www.eyesopen.com