Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution

By A. Radzicka, R. Wolfenden. 1988

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Maximum Allowed Solvent Accessibilites of Residues in Proteins (2012, unknown): “hTransfer energy from cyclohexane to water [29].”
Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane. (2020, background): “A popular approach to overcoming the computational cost of solvent electrostatics models is the Lazaridis implicit membrane model (IMM1 (27)): a Gaussian solvent-exclusion model that uses experimentally measured transfer energies of side-chain analogs in organic solvents to emulate amino acid prefer”
Positioning of proteins in membranes: A computational approach (2006, background): “1971) and has high dielectric constant (;10–20), unlike the hydrocarbon core of lipid bilayers (Benz et al. 1975; Radzicka and Wolfenden 1988).”
BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes (2017, methodology): “Each residue was encoded using its computed volume (16), hydrophobicity (17), polarity (18), together with the relative surface accessibility (RSA) and secondary structure (SS) as predicted by NetSurfP (19) of all the residues in a window of size 9 centered on the residue itself.”
SBSM-Pro: support bio-sequence machine for proteins (2023, methodology): “We first construct a similarity matrix S ∈ R p × p .”