3DPL™ - Fast 3D Virtual Screening
3DPL offers a rapid approach for selecting a population of targeted molecules from starting sets of millions of small molecule structures. 3DPL technology uses a protein structure and large databases of small molecule structures to perform rapid, flexible virtual screening against all likely binding sites on the protein surface. 3DPL is used to identify highly targeted sets of small molecule structures likely to bind the protein surface. Discovery companies can assay sets of hundreds to low thousands of high value structures and avoid screening larger sets of tens of thousands of diverse compounds.

3DPL is designed to allow drug discovery companies to identify a target-focused set of chemistry and move to bioassay and lead identification as quickly and efficiently as possible. 3DPL has four major advantages that allow for rapid identification of potential active molecules:
  • Knowledge of active site not required: 3DPL includes technology for automated identification of all sites on the protein surface of appropriate size for binding with a therapeutic molecule. This Convex Hull technology identifies all potential binding sites that can be used in flexible screening, and it eliminates the need for an identified binding site as input for the screening experiment.
  • Entire protein surface is considered: Each small molecule is compared against all potential binding sites on the 3-D protein surface to look for potential binding interactions. This approach offers the opportunity to identify ligands that would have been overlooked by virtual screening technologies that focus on only one or more pre-defined active sites on the protein surface.
  • Automatic conformational analysis: Each small molecule ligand is flexed, in an energetically directed approach, and re-oriented thousands or millions of times in the search for potential matches between the ligand and the protein surface.
  • Speed enables in silico screening of millions of small molecules: 3DPL employs a unique and patented derivative field grid to direct small molecules to favorable binding conformations. The use of these grids significantly reduces computational time. Running on a single 1.4GHz server, 3DPL is able to evaluate over 8 million chemical structures for binding across the entire protein surface in less than 4 days - a 600-fold increase over the fastest technology available today. Much larger structure sets can be run, which eliminates the need to filter out large numbers of potentially valuable samples before the virtual screening experiment.

The input to the system is a 3-D protein model and a set of 3-D small molecule structures; the output is a selection of scored small molecule structures that have been calculated to show binding affinity for the protein surface. 3DPL can be used with ChemNavigator's iResearch™ Library of over million unique structures to provide access to the greatest diversity of commercially available small molecule compounds.

3DPL provides both an advanced user interface and a simple user interface under the Windows™ operating system.


3DPL Graphical User Interface

To learn more about 3DPL come to the downloads area of the ChemNavigator web site.  Then, download and install 3DPL.  Once installed, the 3DPL User Manual provides details on the operation of 3DPL.

3DPL Highlights
With a 3-D protein model and a set of 3-D small molecule structures 3DPL produces a selection of scored small molecule structures that have been calculated to show binding affinity for the protein surface.

Download 3DPL and try it within your company's research program.

For more information, please contact a business development representative at CNC_Support@sial.com.

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