Table 1.

Predicates used as background knowledge.

Type of information	Predicates	Description
Physico-chemical changes induced by the substitution	modif_size(+mutationid, #value) modif_charge(+mutationid, #value) modif_hydrophobicity(+mutationid, #value) modif_polarity(+mutationid, #value)	Size, charge, polarity and hydrophobicity modifications
	g_p(+mutationid, #gp)	Glycine or proline loss or apparition
Evolutionary features	conservation_wt(+mutationid, −conservationwt)	Percentage of the wild type residue in the alignment column
	conservation_mut(+mutationid, −conservationmut)	Percentage of the mutant residue in the alignment column
	freq_at_pos(+mutationid, −freqatpos)	Number of known mutations at this position
	cluster_5res_size(+mutationid, −cluster5ressize)	Number of mutations at a distance of less than 5 residues in the sequence
Structural features	secondary_struc(+mutationid, #secondary_struc)	Secondary structure element (helix, sheet, no)
	gain_contact(+mutationid, −gaincontact) lost_contact(+mutationid, −lostcontact) identical_contact(+mutationid, −identicalcontact)	Contacts between – the wild type residue and its direct 3D neighbours, based on the wild type 3D model the mutant residue and its direct 3D neighbours, based on the mutant 3D model are computed and compared
	gain_n1_contact(+mutationid, −gainn1contact) lost_n1_contact(+mutationid, −lostn1contact) identical_n1_contact(+mutationid, −identical_n1_contact)	Contacts between – residues in contact with the wild type residue and their direct 3D neighbours, based on the wild type 3D model – residues in contact with the mutant residue and their direct 3D neighbours, based on the mutant 3D model are computed and compared
	wt_accessibility(+mutationid, −wtacc) mut_accessibility(+mutationid, −mutacc)	Accessibility of the wild type/mutant residue
	cluster3d_10(+mutationid, −cluster3d10) cluster3d_20(+mutationid, −cluster3d20) cluster3d_30(+mutationid, −cluster3d30)	Number of mutations in the 3D cluster at 10, 20 and 30 A°
	stability_decrease(+mutationid) stability_increase(+mutationid) reliability_deltag(+mutationid, −reliabilitydeltag)	The change in protein relative stability upon mutation