Key factors for successful generation of protein-fragment structures requirement on protein, crystals, and technology

Methods Enzymol. 2011;493:61-89. doi: 10.1016/B978-0-12-381274-2.00003-0.


In the past two decades, fragment-based approaches have evolved as a predominant strategy in lead discovery. The availability of structural information on the interaction geometries of binding fragments is key to successful structure-guided fragment-to-lead evolution. In this chapter, we illustrate methodological advances for protein-fragment crystal structure generation in order to offer general lessons on the importance of fragment properties and the most appropriate crystallographic setup to evaluate them. We analyze elaborate protocols, methods, and clues applied to challenging complex formation projects. The results should assist medicinal chemists to select the most promising targets and strategies for fragment-based crystallography as well as provide a tutorial to structural biologists who attempt to determine protein-fragment structures.

MeSH terms

  • Binding Sites
  • Crystallization
  • Crystallography, X-Ray
  • Drug Design
  • Drug Discovery / methods
  • Hydrogen Bonding
  • Ligands
  • Models, Molecular
  • Protein Binding
  • Proteins / chemistry*


  • Ligands
  • Proteins