Improved protein-ligand docking using GOLD

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The Chemscore function was implemented as a scoring function for the proteinligand docking program GOLD, and its performance compared to the original Goldscore function and two consensus docking protocols, Goldscore-CS and Chemscore-GS, in terms of docking accuracy, prediction of binding affinities, and speed. In the Goldscore-CS protocol, dockings produced with the Goldscore function are scored and ranked with the Chemscore function; in the Chemscore-GS protocol, dockings produced with the Chemscore function are scored and ranked with the Goldscore function. Comparisons were made for a clean set of 224 proteinligand complexes, and for two subsets of this set, one for which the ligands are drug-like, the other for which they are fragment-like. For drug-like and fragment-like ligands, the docking accuracies obtained with Chemscore and Goldscore functions are similar. For larger ligands, Goldscore gives superior results. Docking with the Chemscore function is up to three times faster than docking with the Goldscore function. Both combined docking protocols give significant improvements in docking accuracy over the use of the Goldscore or Chemscore function alone. Goldscore-CS gives success rates of up to 81% (top-ranked GOLD solution within 2.0 Å of the experimental binding mode) for the clean list, but at the cost of long search times. For most virtual screening applications, Chemscore-GS seems optimal; search settings that give docking speeds of around 0.251.3 min/compound have success rates of about 78% for drug-like compounds and 85% for fragment-like compounds. In terms of producing binding energy estimates, the Goldscore function appears to perform better than the Chemscore function and the two consensus protocols, particularly for faster search settings. Even at docking speeds of around 12 min/compound, the Goldscore function predicts binding energies with a standard deviation of 10.5 kJ/mol. Proteins 2003;52:609623. 2003 Wiley-Liss, Inc.




Verdonk, M. L., Cole, J. C., Hartshorn, M. J., Murray, C. W., & Taylor, R. D. (2003). Improved protein-ligand docking using GOLD. Proteins: Structure, Function and Genetics, 52(4), 609–623.

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