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DeepSMILES

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Prepared for the 6th RDKit UGM Sept 2018 Cambridge, UK

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DeepSMILES

  1. 1. 6th RDKit UGM Cambridge UK Sep 2018 DeepSMILES Noel O’Boyle Andrew Dalke Gómez-Bombarelli et al. Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules. ACS Central Science 2018, 4, 268–276. c1ccccc1 c1ccccc1
  2. 2. 6th RDKit UGM Cambridge UK Sep 2018 DeepSMILES Noel O’Boyle Andrew Dalke Gómez-Bombarelli et al. Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules. ACS Central Science 2018, 4, 268–276. c1ccccc1 c1ccccc1 c1ccccc2c1ccc(cc1c1ccccc1(C)C Invalid syntax
  3. 3. 6th RDKit UGM Cambridge UK Sep 2018 c1ccccc1 c1ccccc1 c1ccccc2c1ccc(cc1c1ccccc1(C)C Invalid syntax DeepSMILES SMILES input DeepSMILES
  4. 4. 6th RDKit UGM Cambridge UK Sep 2018 c1ccccc1 c1ccccc1 c1ccccc1(C)C DeepSMILES SMILES input DeepSMILES
  5. 5. 6th RDKit UGM Cambridge UK Sep 2018 RING CLOSURE Notation SMILES ….c2ccccc2 ….c3ccccc3…c1ccccc1
  6. 6. 6th RDKit UGM Cambridge UK Sep 2018 RING CLOSURE Notation DeepSMILES SMILES …cccccc6 ….c2ccccc2 ….c3ccccc3…c1ccccc1
  7. 7. 6th RDKit UGM Cambridge UK Sep 2018 Branch NOTATION DeepSMILES SMILES c1cccC=O)Cl))cc1 c1ccc(C(=O)Cl)cc1 =O C c c c c1 Cl C c c c c1 c1 c c c c c1 SH Eisman. A Polish-type notation for chemical structures. J. Chem. Doc. 1964, 4, 186. H Hiz. A linearization of chemical graphs. J. Chem. Doc. 1964, 4, 173.
  8. 8. 6th RDKit UGM Cambridge UK Sep 2018 DeepSMILES Noel O’Boyle Andrew Dalke O'Boyle, Noel; Dalke, Andrew (2018): DeepSMILES: An Adaptation of SMILES for Use in Machine-Learning of Chemical Structures. ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv.7097960.v1 pip install deepsmiles https://github.com/nextmovesoftware/deepsmiles

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