A family competition evolutionary algorithm for automated docking of flexible ligands to proteins

Jinn-Moon Yang*, Cheng Yan Kao

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

Abstract

In this paper, we study an evolutionary algorithm for flexible ligand docking. Based on family competition and adaptive rules, the proposed approach consists of global and local strategies by integrating decreasing mutations and self-adaptive mutations. To demonstrate the robustness of the proposed approach, we apply it to the problems of the first international contests on evolutionary optimization. Following the description of function optimization, our approach is applied to a dihydrofolate reductase enzyme with the anti-cancer drug methotrexate and with two analogs of the antibacterial drug trimethoprim. Our numerical results indicate that the proposed approach is robust. The docked lowest energy structures have rms derivations ranging from 0.72 A to 1.98 A with respect to the corresponding crystal structure.

Original languageEnglish
Pages (from-to)225-237
Number of pages13
JournalIEEE Transactions on Information Technology in Biomedicine
Volume4
Issue number3
DOIs
StatePublished - Sep 2000

Keywords

  • Dihydrofolate reductase-methotrexate
  • Family competition
  • Flexible ligand docking
  • Function optimization
  • Genetic algorithms
  • Multiple mutations

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