Surflex-Dock

Ligand-Receptor Docking and Virtual Screening

Now Available Fully Integrated with SYBYL^® !

Overview

Screening large compound libraries remains an expensive and time-consuming task. Computational high-throughput screening can enrich the fraction of suitable compounds in a screening collection, thereby reducing the cost of biological testing in lead discovery.

Surflex-Dock™ offers unparalleled enrichments in virtual high-throughput screening combined with state-of-the-art speed, accuracy and usability. It uses an updated and re-parameterized empirical scoring function (based on the Hammerhead docking system) with additional negative training data and a search engine that relies on a surface-based molecular similarity method.

Surflex-Dock has been extensively validated and favorably compared to all leading competing methods by independent researchers (Kellenberger et al., (2004) Proteins: Structure, Function, and Bioinformatics 57, 225-242), along with 28 other studies by the applications author, Prof. Ajay N. Jain, Ph.D., a faculty member at the University of California San Francisco Cancer Research Institute.

"Surflex-Dock couples a unique scoring function with a patented state-of-the-art search engine. The combination has been shown to yield excellent results in terms of docking accuracy, and distinctively superior results in terms of screening enrichment," said Prof. Ajay N. Jain.

Surflex-Dock is now fully integrated into Tripos' market-leading SYBYL product, and available for immediate release on Tripos' Download site.

Surflex Brochure (76k)

Influenza virus neuraminidase (1B9V) in complex with an inhibitor (purple capped sticks). The minimized inhibitor has been redocked by Surflex-Dock into the protein (yellow capped sticks) with an rms deviation of 0.645 Angstroms.

Key Benefits

• Accurate Scoring - Scoring function is derived from known binding affinity data and negative training data to reduce false positive binding scores
• Speed - On average 17s per ligand (~3s per rotatable bond)
• Easier Protein Preparation - Protein structure preparation is simple and part of the docking workflow
• Easier Docking Preparation - Docking gives good results with default settings
• Protomol guided docking - Docking is guided by a 'protomol' which can be automatically generated and/or user-defined
• Ring Flexing - Generic ring conformations are applied to each flexible ring system, and the resulting conformations are minimized
• Parallelization - A simple parallelization protocol exists to enable the use of multiple processors