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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)
     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