Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine

J Med Chem. 2003 Feb 13;46(4):499-511. doi: 10.1021/jm020406h.


Surflex is a fully automatic flexible molecular docking algorithm that combines the scoring function from the Hammerhead docking system with a search engine that relies on a surface-based molecular similarity method as a means to rapidly generate suitable putative poses for molecular fragments. Results are presented evaluating reliability and accuracy of dockings compared with crystallographic experimental results on 81 protein/ligand pairs of substantial structural diversity. In over 80% of the complexes, Surflex's highest scoring docked pose was within 2.5 A root-mean-square deviation (rmsd), with over 90% of the complexes having one of the top ranked poses within 2.5 A rmsd. Results are also presented assessing Surflex's utility as a screening tool on two protein targets (thymidine kinase and estrogen receptor) using data sets on which competing methods were run. Performance of Surflex was significantly better, with true positive rates of greater than 80% at false positive rates of less than 1%. Docking time was roughly linear in number of rotatable bonds, beginning with a few seconds for rigid molecules and adding approximately 10 s per rotatable bond.

Publication types

  • Comparative Study

MeSH terms

  • Algorithms
  • Binding Sites
  • Crystallography, X-Ray
  • Herpesvirus 1, Human / chemistry
  • Ligands*
  • Models, Molecular
  • Proteins / chemistry*
  • Quantitative Structure-Activity Relationship*
  • Receptors, Estrogen / antagonists & inhibitors
  • Receptors, Estrogen / chemistry
  • Thymidine Kinase / chemistry


  • Ligands
  • Proteins
  • Receptors, Estrogen
  • Thymidine Kinase