Included Methods

Valdar

Protein Conservation Metrics described in the paper by Valdar [1]:

  • KABAT (Wu and Kabat, 1970)
  • JORES (Jores et al., 1990)
  • SCHNEIDER (Schneider, 1997)
  • SHENKIN (Shenkin et al., 1991)
  • GERSTEIN (Gerstein and Altman, 1995)
  • TAYLOR_GAPS (Taylor, 1986)
  • TAYLOR_NO_GAPS (Taylor, 1986)
  • ZVELIBIL (Zvelibil et al., 1987)
  • KARLIN (Mirny and Shakhnovich, 2001)
  • ARMON (Armon et al., 2001)
  • THOMPSON (Thompson et al., 1997)
  • NOT_LANCET (Pilpel and Lancet, 1999)
  • MIRNY (Mirny and Shakhnovich, 1999)
  • WILLIAMSON (Williamson, 1995)
  • LANDGRAF (Landgraf et al., 1999)
  • SANDER (Sander and Schneider, 1991)
  • VALDAR (Valdar and Thornton, 2001)

SMERFS

A method for predicting protein functional sites developed in the Barton Group [2]:

  • SMERFS (Manning et al., 2008, more about available custom parameters here)

References

[1]Valdar, W. S. J. Scoring residue conservation. Proteins: Structure, Function, and Genetics 48, 227–241 (2002). DOI: 10.1002/prot.10146
[2]Manning, J. R., Jefferson, E. R. & Barton, G. J. The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction. BMC Bioinformatics 9, 51 (2008). DOI: 10.1186/1471-2105-9-51