The structural dependence of amino acid hydrophobicity parameters

PDZ Domain-containing 1 (PDZK1) Protein Regulates Phospholipase C-β3 (PLC-β3)-specific Activation of Somatostatin by Forming a Ternary Complex with PLC-β3 and Somatostatin Receptors

“…Subsequently, pocket residues were identified according to pocket definitions described by Wiedemann et al (26). Pocket residues of PDZ domains were analyzed by using 10 physicochemical properties of amino acids that describe the number of hydrogen bond donors (27), polarity (28), volume (28), bulkiness (29), hydrophobicity (29,30), isoelectric point (29), positive charge (27), negative charge (27), electron ion interaction potential (31), and free energy in water (32).…”

It Is Important to Compute Intramolecular Hydrogen Bonding in Drug Design?

“…The approaches span from simple indicator methods [287,288] to parametrization approaches using theoretically calculated properties, such as atomic charges [289], molecular electrostatic potential [290], LUMO and HOMO properties [289,291], atom polarizability [292], and superdelocalizability [263,293], to model hydrogen bond strength. However, due to the character of being the property of a group of atoms and the susceptibility to local environments, hydrogen bonds could not be modeled accurately by a general semiempirical or rule-based method because there are many exceptions, such as steric factors, to be accommodated by a finite set of rules.…”

The interplay of descriptor-based computational analysis with pharmacophore modeling builds the basis for a novel classification scheme for feruloyl esterases

“…T he different amino acid properties used as autocorrelation descriptors were various types of amino acids indices viz., hydrophobicity scales (Cid et al, 1992), average flexibility indices (Bhaskaran and Ponnuswamy, 1988), polarizability parameter (Charton M and Charton BI , 1982), free energy of solution in water (Charton M and Charton BI , 1982), residue accessible surface area in tripeptide (Chothia, 1976), residue volume (Bigelow, 1967), steric parameter (Charton, 1981) and relative mutability (Dayhoff et al, 1979). T hree different autocorrelation descriptors viz., Moreau-Broto autocorrelation, Moran autocorrelation and Geary autocorrelation descriptors are computed, each having 240 descriptor components.…”