Molecular replacement using ab initio polyalanine models generated with ROSETTA

Acta Crystallogr D Biol Crystallogr. 2008 Dec;64(Pt 12):1288-91. doi: 10.1107/S0907444908033192. Epub 2008 Nov 18.

Abstract

The success of the molecular-replacement method for solving protein structures from experimental diffraction data depends on the availability of a suitable search model. Typically, this is derived from a previously solved structure, sometimes by homology modelling. Very recently, Baker, Read and coworkers have demonstrated a successful molecular-replacement case based on an ab initio model generated by ROSETTA [Qian et al. (2007), Nature (London), 450, 259-264]. In this contribution, a number of additional test cases in which ab initio models generated using modest computational resources give correct molecular-replacement solutions are reported. Unsuccessful cases are also reported for comparison and the factors influencing the success of this route to structure solution are discussed.

MeSH terms

  • Computer Simulation
  • Crystallization
  • Crystallography, X-Ray / instrumentation
  • Crystallography, X-Ray / methods*
  • Electronic Data Processing
  • Forecasting
  • Information Management
  • Models, Molecular*
  • Peptides / chemistry*
  • Software Validation
  • Software*
  • Structural Homology, Protein

Substances

  • Peptides
  • polyalanine