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Ligand Shape-based alignment of small molecules is a widely used approach in computer-aided drug discovery, such as search accessible chemical space to find analogues to the hit series, or discovery new chemical starting points for a novel target.
The critical feature of a ligand similarity algorithm is to efficiently discern active and similar inactive compounds during the screening of large Databases. 
4Dshape+ Sim GUI
Datawarrior plugin for linux and windows.

4Dshape+ Similarity Module

Fast, effective multiple ligands shape-based screening

4Dshape+ Sim module uses the 3D chemical features of active and inactive ligands to create a 4D-fingerprint (3D-structures + 1D inactive structures) which can then be used in multiple ligand shape-based similarity search. 
Features and Applications of 4Dshape+  similarity module:
  • Quickly locates plausible and unique pharmacophores of the active ligands in which pharmacophores from similar inactive ligands (decoys) are removed.
  • Generates a unique fingerprint of multiple-ligands features using the proprietary 4D-fingerprints algorithm.
  • Screen Databases using the fingerprint of single or multiple active molecules  (Queries).
  • The ligand structures are treated flexible during the similarity search.
  • Virtual screening combines structural flexibility on-the-fly and/or ensemble of conformers of the ligand database to accurately prioritize chemical structures with diverse shapes, sizes, and composition (“scaffold hopping”).
  • Swiftly and accurately prioritizes chemical structures  by screening databases of billions of molecules.  
  • Predicts off-target (Drug Repurposing) and selectivity of lead compounds (toxicity prediction).
  • Provides accurate Multiple ligand shape-based alignment for 3D-QSAR application.
  • Fast screening of  small molecule libraries using multiple bound ligands to the receptor in a single run.
  • Includes an on-the-fly tunable Scoring function to better suit the structural scaffolds of interest. 
  • Provides a rapid pre-screening tool that can be seamlessly  integrated with molecular docking.
  • Easily runs the similarity search module and visualizes the results using the Datawarrior plugin.​
Multiple ligand shape-based search algorithm produce higher early enrichment than traditional single query similarity. 
Hit rate (HR) Result at 1% of DUDE database (102 targets) using multiple queries-shape based 4Dshape+ Sim module.
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