Table 1

Attributes used for predicting functional effects of missense mutations

Abbreviation

Type

Description

Information


effect

Discrete

Effect of mutation on functionality

Class


ac

Continuous

Solvent accessible area of native AA

rac

Continuous

Accessibility relative to maximum accessibility in training set

bf

Continuous

Normalised B-factor of native AA

nbf

Continuous

Normalised B-factor of structural neighbourhood of native AA

Structural

bur

Discrete

Mutant AA is charged AA at buried site

trn

Discrete

Mutant AA occurs at glycine or proline in a turn

hlx

Discrete

Mutant AA occurs in helical region and involves glycine or proline

ifc

Discrete

Native AA is near subunit interface


nrent

Continuous

Phylogenetic entropy of structural neighbourhood of native AA

Structural + Evolutionary


rent

Continuous

Normalised phylogenetic entropy of native AA

cnsd

Discrete

Native AA is at conserved position in phylogenetic profile

ncnsd

Discrete

Native AA is near conserved position in phylogenetic profile

Evolutionary

uslaa

Discrete

Mutant AA is not in phylogenetic profile

uslby

Discrete

Mutant AA is not in the smallest AA class that includes the phylogenetic profile


Needham et al. BMC Bioinformatics 2006 7:405   doi:10.1186/1471-2105-7-405

Open Data