Yucca: An Efficient Algorithm for Small-Molecule Docking

Chem Biodivers. 2005 Nov;2(11):1517-24. doi: 10.1002/cbdv.200590123.


In this paper, we present a new algorithm, which is based on an efficient heuristic for local search, for rigid protein-small-molecule docking. We tested our algorithm, called Yucca, on the recent 100-complex benchmark, using the conformer generator OMEGA to generate a set of low-energy conformers. The results showed that Yucca is competitive both in terms of algorithm efficiency and docking accuracy.

MeSH terms

  • Algorithms*
  • Binding Sites / physiology
  • Models, Biological*
  • Molecular Structure
  • Protein Binding / physiology
  • Proteins / chemistry
  • Proteins / metabolism


  • Proteins