Prediction of α-Helices in Proteins with the Hydrophobic Strip-of-Helix Template and Distributions of Other Amino Acids around the Hydrophobic Strip

Visual Molecular Dynamics Investigations of the Impact of Hydrophobic Nanoparticles on Prognosis of Alzheimer’s Disease and Cancers

“…residues are inserted at each of the gap position identified by IALIGN, an interactive alignment program distributed with the Protein Identification Resource (PIR; Eleanor M.B, 1994) This model was compared with DgA-I, HuA-I and ChA-I resprsenting canine, human andchicken Apo A-I respectively. Results were then compared using a "strip of the helix" template(Vazquez et al 1992) by scoring 1 or 0 for residues that did , or did not, fit into the template.…”

Deciphering the structural code for proteins: Helical propensities in domain classes and statistical multiresidue information in α‐helices

“…In earlier reports, the characteristic distribution of hydrophobic and hydrophilic residues in different secondary structure segments was the basis on which methods for predicting secondary structure were tested (Lim, 1974b;Cid et al, 1982). More recently, the effect on helix formation of patterns of hydrophobic and nonhydrophobic side chains in protein sequences has been studied in different ways (Torgerson et al, 1991;Kamtekar et al, 1993;Vazquez et al, 1993a;1993b;West & Hecht, 1995;Xiong et al, 1995). Torgerson et al (1991) predicted quadrant orientations of amino acids in most a-helices, and reported that the templatepredicted configurations closely match crystallographic data on a-helices.…”

“…Torgerson et al (1991) predicted quadrant orientations of amino acids in most a-helices, and reported that the templatepredicted configurations closely match crystallographic data on a-helices. Vazquez et al (199%) reported the presence of favored or suppressed side-chain patterns within protein sequences in relation with a-helices and &strands and also developed an a-helix predictor (Vazquez et al, 1993a). which was based on the identification of a longitudinal, hydrophobic strip-of-helix pattern.…”