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Table 3 Influence of mutations as predicted by the solvation energy based approach compared with the literature. For each of the five protein structures in the first column, we listed the text mined protein point mutations and the manually extracted effect of this mutation as reported in the literature. We compared these effects with the stability change prediction by our model and evaluated if these were in compliance. In 71% of the cases a change in function or stability is correlated with interaction energy.

From: Improved mutation tagging with gene identifiers applied to membrane protein stability prediction

Protein name Mutation in literature Effect as reported in literature Stability change Compliance
Bacteriorhodopsin
PDB: 1brr
UniProt: P02945
G113Q destabilized slightly destabilizing yes
  G113L destabilized destabilizing yes
  G116Q destabilized slightly destabilizing yes
  G116L destabilized destabilizing yes
  I117F destabilized slightly destabilizing yes
  I117A destabilized stabilizing no
  M145F still active destabilizing no
Halorhodopsin
PDB: 1e12
UniProt: P16102
H95A destabilized slightly destabilizing yes
  H95R destabilized slightly stabilizing no
  R108Q not functional slightly destabilizing yes
  T203V less active destabilizing yes
Rhodospin
PDB: 1f88
UniProt: P02699
T93P misfolded destabilizing yes
  T94I night blindness destabilizing yes
  C110F r. pigmentosa destabilizing yes
  C110Y r. pigmentosa destabilizing yes
  C110A r. pigmentosa slightly destabilizing yes
  E122Q still active slightly destabilizing no
  E122D still active slightly destabilizing no
  E122A   slightly destabilizing  
  E122R no retinal binding slightly destabilizing yes
  C185A wrong disulfide slightly destabilizing yes
  G188R misfolding slightly destabilizing yes
  S186A incr. activation energy slightly destabilizing yes
  C187Y r. pigmentosa destabilizing yes
  C187A r. pigmentosa slightly destabilizing yes
  N310C less activity slightly destabilizing yes
  M317C less activity slightly destabilizing yes
Antiporter
PDB: 1zcd
UniProt: P13738
A130C   slightly stabilizing  
  D133A not functional slightly destabilizing yes
  H225P less activity destabilizing yes
  H225C less activity none no
  G303C not functional slightly destabilizing yes
Aquaporin
PDB: 1h6i
UniProt: P29972
N42A still active slightly destabilizing no
  A73M not functional slightly stabilizing no
  Y186F conduct water slightly destabilizing  
  Y186A no water conductance stabilizing  
  Y186N no water conductance stabilizing  
  C189M less activity slightly stabilizing no
  C189S still active slightly stabilizing yes
  H209A still active slightly destabilizing no