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 |