Sep 9, 2010

Performance of phased rotation, conformation and translation function: accurate protein model building with tripeptidic and tetrapeptidic fragments

Acta Crystallographica. Section D, Biological Crystallography
Frantisek Pavelcik, Jirí Václavík

Abstract

The automatic building of protein structures with tripeptidic and tetrapeptidic fragments was investigated. The oligopeptidic conformers were positioned in the electron-density map by a phased rotation, conformation and translation function and refined by a real-space refinement. The number of successfully located fragments lay within the interval 75-95% depending on the resolution and phase quality. The overlaps of partially located fragments were analyzed. The correctly positioned fragments were connected into chains. Chains formed in this way were extended directly into the electron density and a sequence was assigned. In the initial stage of the model building the number of located fragments was between 60% and 95%, but this number could be increased by several cycles of reciprocal-space refinement and automatic model rebuilding. A nearly complete structure can be obtained on the condition that the resolution is reasonable. Computer graphics will only be needed for a final check and small corrections.

  • References35
  • Citations1

References

  • References35
  • Citations1

Citations

Mentioned in this Paper

Electron Density
Oligopeptides
Crystallography, X-Ray
Protein Conformation
Fragments

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