Cheminformatic Tools and Databases for Pharmacology
 
Shape-based alignment of molecules with SenSaaS


Reference:

Douguet D. and Payan F., SenSaaS: Shape-based Alignment by Registration of Colored Point-based Surfaces, Molecular Informatics, 2020, 8, 2000081.

doi: 10.1002/minf.202000081

and the code is available on GitHub at sensaas project.




- Molecules are represented as colored point-based vdW surfaces

- Geometric and Color fitness scores are calculated

- SenSaaS possesses sub-matching properties (alignment of substructures or small fragments)

- If you want to screen a library of molecules, you can also use the LEA3D tool and select the Shape similarity function



 

 1) Upload the reference molecule which remains fixed during the alignment
  • Molecular structure file with hydrogens and 3D coordinates (you can use this drawing tool):

    SDF file format with one structure:  

  •  
  • (option) conformers for the reference structure (! that will change the coordinates and the referential of the molecule):

    Generate conformers with RDKit (maximum number of conformers = )


  •  2) Upload the second molecule which will move
  • Molecular structure file with hydrogens and 3D coordinates (you can use this drawing tool):

    SDF file format with one structure:  

    Keep rigid (default)

    Flexible alignment by optimizing the conformer

  •  
  • (option) conformers for the structure:

    Generate conformers with RDKit (maximum number of conformers = )


  • (option) repeats [1-100] to display alternative alignments when they exist (eg: aligning a fragment on a large molecule)

     



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