Structure-Based Drug Design pp 223-232

Part of the NATO ASI Series book series (NSSE, volume 352) | Cite as

Computational Approaches to Modeling Receptor Flexibility Upon Ligand Binding: Application to Interfacially Activated Enzymes

  • R. C. Wade
  • V. Sobolev
  • A. R. Ortiz
  • G. Peters

Abstract

Receptors generally undergo conformational change upon ligand binding. We describe how fairly simple techniques may be used in docking and design studies to account for some of the changes in the conformations of proteins on ligand binding. Simulations of protein-ligand interactions that give a more complete description of the dynamics important for ligand binding are then discussed. These methods are illustrated for phospholipase A2 and lipase, enzymes that both undergo interfacial activation.

Abbreviations

BD

Brownian dynamics

HSF-PLA2

human synovial fluid phospholipase A2

MD

molecular dynamics

nmr

nuclear magnetic resonance

QSAR

quantitative structure activity relationship

rmsd

root mean square deviation

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Copyright information

© Springer Science+Business Media Dordrecht 1998

Authors and Affiliations

  • R. C. Wade
    • 1
  • V. Sobolev
    • 2
  • A. R. Ortiz
    • 1
  • G. Peters
    • 3
    • 4
  1. 1.European Molecular Biology LaboratoryHeidelbergGermany
  2. 2.Department of Plant GeneticsWeizmann Institute of ScienceRehovotIsrael
  3. 3.Chemistry DepartmentUniversity of CopenhagenCopenahagenDenmark
  4. 4.Novo NordiskBagsvaerdDenmark

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