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Table 1 List of amino acid descriptors available in PsychoProt. Only sets 1 and 2 are recommended for normal use

From: Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server

Set 1

Physicochemical descriptors

Set 3

Composite physicochemical descriptors

 

 Volume

 

 Volume/P(helix)

 

 Log(solubility)

 

 Volume/P(sheet)

 

 Hydrophobicity

 

 Volume/log(solubility)

 

 Isoelectric point

 

 Log(solubility) x Flexibility

 

 P(helix)

 

 Steric hindrance x Flexibility

 

 Steric hindrance

 

 P(helix) + P(sheet)

 

 P(sheet)

 

 log(solubility) x Hydrophobicity

 

 Flexibility

 

 Hydrophobicity x Flexibility

Set 2

Metabolic descriptors

 

 Volume/(P(helix) + P(sheet))

 

 In vivo decay time

 

 Steric hindrance/P(helix)

 

 Cost for synthesis

 

 Isoelectric point/P(sheet)

   

 Volume x Isoelectric Point

   

 Isoelectric point/P(helix)

   

 P(helix)/P(sheet)

   

 Steric hindrance/P(sheet)

   

 P(helix) x Flexibility

  

Set 4

Discrete descriptors

   

 Number of Oxygen atoms in side chain

   

 Number of Nitrogen atoms in side chain

   

 Number of Sulfur atoms in side chain

   

 Number of H-bond donors and acceptors in side chain

  1. Set 3 extends Set 1 by including precomputed combinations of its descriptors (such as Volume/P(helix)). Set 4 consists of discrete numbers describing the heavy atom compositions of the amino acid side chains. Sets 3 and 4 are experimental and should be used with caution, since many of their descriptors are correlated to those in Sets 1 and 2. Note also that including more descriptors increases the strength of the Bonferroni correction