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case study

The following molecules were used as decoy in VEGFR2 of the DEKOIS 2.0 [1] and were used to test MolToPDBQTBlock and MolFromPDBQTBlock function in the watvina/rdkit2pdbqt.py[2].

  1. ZINC20533791
    2. ZINC20533791

    ZINC ID: 20533791

    SMILES: [H]/N=C1/SC(C(=O)Nc2ccc(C(=O)[O-])cc2)CC(=O)N1/N=C/c1c[nH]c2ccccc12

  2. ZINC22579716
    3. ZINC22579716

    ZINC ID: 22579716

    SMILES: Cc1ccc(C2CC(C(F)(F)F)n3nc(C(=O)N4CC[NH+]5CCCC5C4)c(Cl)c3N2)cc1

  3. ZINC08441965
    4. ZINC22579716

    ZINC ID: 08441965

    SMILES: [H]/N=C1\C(C#N)C2=CC[NH+](Cc3ccccc3)CC2C(c2ccc(OC)c3ccccc23)C1(C#N)C#N

Step to reproduce the results

python docking.py

Reference

(1) Bauer, M. R.; Ibrahim, T. M.; Vogel, S. M.; Boeckler, F. M. Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 – A Public Library of Challenging Docking Benchmark Sets. J. Chem. Inf. Model. 2013, 53 (6), 1447–1462. https://doi.org/10.1021/ci400115b.

(2)https://github.com/biocheming/watvina

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