Surface and inside volumes in globular proteins

By Joël Janin. 1979

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Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0 (2018, methodology): “…net charge Grand average of hydropathicity (GRAVY, Kyle and Doolittle, 1982) ProtParam (Gasteiger et al ., 2005) Average of surface exposure (Janin, 1979) Amino acid groupings and scales taken from Composition Profiler (Vacic et al ., 2007) Average of disorder propensity (Dunker et al .,…”
Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 (2020, unknown): “We assessed the change in hydrophobicity and charge of amino acid residues arising due to homoplastic non-synonymous mutations using the hydrophobicity scale proposed by Janin (Janin, 1979).”
Sequence complexity of disordered protein (2001, background): “31 attributes in the initial pool included the 20 amino acid compositions, two different hydropathy scales,(49,50) flexibility index,(51) a-moment,(52) b-moment,(53) net charge (K 1 R 2 D 2 E),(54) aromatic composition (W 1 F 1 Y),(54) coordination number,(55) codon number,(56) alphabet size,(57) an”
Composition Profiler: a tool for discovery and visualization of amino acid composition differences (2007, background): “Physico-chemical and structural properties In addition to the ability to determine enrichment or depletion patterns of individual amino acids, Composition Profiler can also detect enrichment or depletion of groups of amino acids classified by aromaticity, charge, polarity (Zimmerman index [5]), hydr”
EffectorP 3.0: prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes (2021, methodology): “…(K, R) in the sequence; 4) % of negatively charged amino acids (D, E) in the sequence; 5) average surface exposure of amino acids in the sequence (Janin, 1979); 6) average hydrophobicity of amino acids in the sequence (Fauchere & Pliska, 1983); 7) average polarity of amino acids in the sequence…”
Statistical potentials extracted from protein structures: how accurate are they? (1996, methodology): “As Janin (1979) first noted, apparent interior-exterior ‘‘partition energies’’ (extracted from frequencies of amino acids in buried and (Figure 5(b) and (c)) as extracted from the PDB by Hendlich et al. (1990).”
Computational modeling of membrane proteins (2014, background): “45,49,50 The experimental scales, that previously used single residues or small peptides, were recently expanded by measuring partitioning energies of amino acids in fully folded proteins: (1) the biological hydrophobicity scale developed by White and von Heijne measures the partitioning of…”
The importance of intrinsic disorder for protein phosphorylation. (2004, background): “Each residue was assigned a property: surface or buried (28) (Fig.”