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


References:

  • Biyuzan H., Masrour M.-A., Grandmougin L., Payan F. and Douguet D., SENSAAS-Flex: a joint optimization approach for aligning 3D shapes and exploring the molecular conformation space, Bioinformatics, 2024, 40:3, btae105.

    doi: 10.1093/bioinformatics/btae105

  • 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

  • The code for the rigid version is available on GitHub at sensaas project and the code for the flexible version is available from the link given in the publication SENSAAS-Flex.



- 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 (eg: FDA-approved drugs), please 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 l) performs [1-10] calculation(s) but only the best results will be selected

  • (option r) repeats [1-100] to display alternative alignments - useful for aligning 1 fragment on 1 large molecule

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