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Improving Torsion Library Patterns with SMARTScompare

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Improving Torsion Library Patterns with SMARTScompare

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Patrick Penner
13 / 06 / 2022 1
MIN FACULTY
Center for BIOINFORMATICS
Improving Torsion Library Patterns
with SMARTScompare
Patrick Penner
Patrick Penner
13 / 06 / 2022 2
MIN FACULTY
Center for BIOINFORMATICS
Classifying Torsions
2ANS
Patrick Penner
13 / 06 / 2022 3
MIN FACULTY
Center for BIOINFORMATICS
Classifying Torsions
2ANS
Patrick Penner
13 / 06 / 2022 4
MIN FACULTY
Center for BIOINFORMATICS
Torsion Library
Penner et al. (2022). J. Chem. Inf. Model.
Guba et al. (2016). J. Chem. Inf. Model.
Schärfer et al. (2013). J. Med. Chem.
Patrick Penner
13 / 06 / 2022 5
MIN FACULTY
Center for BIOINFORMATICS
Matching
Patrick Penner
13 / 06 / 2022 6
MIN FACULTY
Center for BIOINFORMATICS
Matching
Cambridge Structural Database (CSD) Protein Data Bank (PDB)
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Improving Torsion Library Patterns with SMARTScompare

  • 1. Patrick Penner 13 / 06 / 2022 1 MIN FACULTY Center for BIOINFORMATICS Improving Torsion Library Patterns with SMARTScompare Patrick Penner
  • 2. Patrick Penner 13 / 06 / 2022 2 MIN FACULTY Center for BIOINFORMATICS Classifying Torsions 2ANS
  • 3. Patrick Penner 13 / 06 / 2022 3 MIN FACULTY Center for BIOINFORMATICS Classifying Torsions 2ANS
  • 4. Patrick Penner 13 / 06 / 2022 4 MIN FACULTY Center for BIOINFORMATICS Torsion Library Penner et al. (2022). J. Chem. Inf. Model. Guba et al. (2016). J. Chem. Inf. Model. Schärfer et al. (2013). J. Med. Chem.
  • 5. Patrick Penner 13 / 06 / 2022 5 MIN FACULTY Center for BIOINFORMATICS Matching
  • 6. Patrick Penner 13 / 06 / 2022 6 MIN FACULTY Center for BIOINFORMATICS Matching Cambridge Structural Database (CSD) Protein Data Bank (PDB)
  • 7. Patrick Penner 13 / 06 / 2022 7 MIN FACULTY Center for BIOINFORMATICS Matching [cH1:1][c:2]([cH0])!@[NX3:3][a:4]
  • 8. Patrick Penner 13 / 06 / 2022 8 MIN FACULTY Center for BIOINFORMATICS SMARTScompare Schmidt et al (2019). J. Chem. Inf. Model.
  • 9. Patrick Penner 13 / 06 / 2022 9 MIN FACULTY Center for BIOINFORMATICS Benzamidine Example
  • 10. Patrick Penner 13 / 06 / 2022 10 MIN FACULTY Center for BIOINFORMATICS Benzamidine Example [c:2][C:3](=N)(-N) [cH0:1][c:2]([cH0])!@[C:3](=[N:4])(-N) Subclass Pattern Pattern with Incomplete Amidine
  • 11. Patrick Penner 13 / 06 / 2022 11 MIN FACULTY Center for BIOINFORMATICS Benzamidine Example
  • 12. Patrick Penner 13 / 06 / 2022 12 MIN FACULTY Center for BIOINFORMATICS Sorting Example [*:1]~[NX2:2]!@[OX2:3]~[*:4] [*:1]~[nX3:2]!@[OX2:3]~[*:4] [*:1]~[N,n:2]!@[S:3]~[*:4] [*:1]~[NX2:2]!@[SX4:3]~[*:4] [*:1]~[NX2:2]!@[SX3:3]~[*:4] [*:1]~[NX2:2]!@[SX2:3]~[*:4] [*:1]~[N,n:2]!@[P:3]~[*:4] [*:1]~[OX2:2]!@[SX4:3]~[*:4] [*:1]~[OX2:2]!@[SX3:3]~[*:4]
  • 13. Patrick Penner 13 / 06 / 2022 13 MIN FACULTY Center for BIOINFORMATICS Sorting Example [*:1]~[NX2:2]!@[OX2:3]~[*:4] [*:1]~[nX3:2]!@[OX2:3]~[*:4] [*:1]~[N,n:2]!@[S:3]~[*:4] [*:1]~[NX2:2]!@[SX4:3]~[*:4] [*:1]~[NX2:2]!@[SX3:3]~[*:4] [*:1]~[NX2:2]!@[SX2:3]~[*:4] [*:1]~[N,n:2]!@[P:3]~[*:4] [*:1]~[OX2:2]!@[SX4:3]~[*:4] [*:1]~[OX2:2]!@[SX3:3]~[*:4]
  • 14. Patrick Penner 13 / 06 / 2022 14 MIN FACULTY Center for BIOINFORMATICS Sorting Example [*:1]~[NX2:2]!@[SX2:3]~[*:4] [*:1]~[NX2:2]!@[SX3:3]~[*:4] [*:1]~[NX2:2]!@[SX4:3]~[*:4]
  • 15. Patrick Penner 13 / 06 / 2022 15 MIN FACULTY Center for BIOINFORMATICS Sorting Example [*:1]~[NX2:2]!@[OX2:3]~[*:4] [*:1]~[nX3:2]!@[OX2:3]~[*:4] [*:1]~[N,n:2]!@[S:3]~[*:4] [*:1]~[NX2:2]!@[SX4:3]~[*:4] [*:1]~[NX2:2]!@[SX3:3]~[*:4] [*:1]~[NX2:2]!@[SX2:3]~[*:4] [*:1]~[N,n:2]!@[P:3]~[*:4] [*:1]~[OX2:2]!@[SX4:3]~[*:4] [*:1]~[OX2:2]!@[SX3:3]~[*:4] [*:1]~[NX2:2]!@[OX2:3]~[*:4] [*:1]~[nX3:2]!@[OX2:3]~[*:4] [*:1]~[NX2:2]!@[SX4:3]~[*:4] [*:1]~[NX2:2]!@[SX3:3]~[*:4] [*:1]~[NX2:2]!@[SX2:3]~[*:4] [*:1]~[N,n:2]!@[S:3]~[*:4] [*:1]~[N,n:2]!@[P:3]~[*:4] [*:1]~[OX2:2]!@[SX4:3]~[*:4] [*:1]~[OX2:2]!@[SX3:3]~[*:4] Pattern Matches Before Matches After [*:1]~[N,n:2]!@[S:3]~[*:4] 2253 983 [*:1]~[NX2:2]!@[SX4:3]~[*:4] 0 1004 [*:1]~[NX2:2]!@[SX3:3]~[*:4] 0 135 [*:1]~[NX2:2]!@[SX2:3]~[*:4] 0 131 Sort
  • 16. Patrick Penner 13 / 06 / 2022 16 MIN FACULTY Center for BIOINFORMATICS Torsion Tooling
  • 17. Patrick Penner 13 / 06 / 2022 17 MIN FACULTY Center for BIOINFORMATICS Torsion Tooling (https://torsions.zbh.uni-hamburg.de)
  • 18. Patrick Penner 13 / 06 / 2022 18 MIN FACULTY Center for BIOINFORMATICS Thank you for your attention Research Group for Computational Molecular Design: Patrick Penner, Matthias Rarey, Roche: Wolfgang Guba Agnes Meyder Martin Stahl BioSolveIT: Robert Schmidt
  • 19. Patrick Penner 13 / 06 / 2022 19 MIN FACULTY Center for BIOINFORMATICS Additional Reading and Software Availability TorsionAnalyzer Server: https://torsions.zbh.uni-hamburg.de NAOMI ChemBio Suite: https://uhh.de/naomi SMARTS Pattern Analyzer Server https://smarts.plus Modeling Support Server: https://proteins.plus Github: https://github.com/rareylab
  • 20. Patrick Penner 13 / 06 / 2022 20 MIN FACULTY Center for BIOINFORMATICS 1. C. Schärfer, T. Schulz-Gasch, H.-C. Ehrlich, W. Guba, M. Rarey, and M. Stahl, “Torsion Angle Preferences in Druglike Chemical Space: A Comprehensive Guide,” Journal of Medicinal Chemistry, vol. 56, no. 5, pp. 2016–2028, 2013, doi: https://doi.org/10.1021/jm3016816. 2. W. Guba, A. Meyder, M. Rarey, and J. Hert, “Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules for Assessing Conformations of Small Molecules,” Journal of Chemical Information and Modeling, vol. 56, no. 1, pp. 1–5, 2016, doi: https://doi.org/10.1021/acs.jcim.5b00522. 3. P. Penner, W. Guba, R. Schmidt, A. Meyder, M. Stahl, and M. Rarey, “The Torsion Library: Semiautomated Improvement of Torsion Rules with SMARTScompare,” Journal of Chemical Information and Modeling, 2022-03, doi: https://doi.org/10.1021/acs.jcim.2c00043. 4. R. Schmidt, E. S. R. Ehmki, F. Ohm, H.-C. Ehrlich, A. Mashychev, and M. Rarey, “Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms,” Journal of Chemical Information and Modeling, vol. 59, no. 6, pp. 2560–2571, 2019, doi: https://doi.org/10.1021/acs.jcim.9b00250. References