Journal of Computational Chemistry · 1996 · 37 citations · 38 references
Life SciencesBiochemistryChemistryComputational ChemistryStructural BiochemistryStructural BiologyConformational AnalysisConformational ChangeProtein ConformationProtein StructureProtein Structure ModelingSecondary StructureBackbone-dependent RotamersMolecular Modeling Of Amino Acid ConformationsPeptide Structure AnalysisPotential Energy CurvesRamachandran AnalysisRamachandran Plot AnalysisSide Chain ConformationSide-chain Conformation Prediction
Multidimensional conformational analysis (MDCA) predicted the existence of nine stable backbone conformations (αL, αD, βL, γL, γD, δL, δD, ϵL, and ϵD) on the 2D-Ramachandran map, E = E(ϕ, ψ), for a single amino acid diamide (HCONH-CHR-CONH2). The potential energy hypersurfaces (E = E[ϕ, ψ, χ1, χ2]) of For-L-Ser-NH2 associated with the αL-, bgr;L-, γL-, δL-, and ϵL-type stable backbone orientations are investigated in this article. An appropriate number of side-chain rotamers is associated with each of the backbone conformers. In the case of serine, where R = −CH2OH, the two sidechain torsional angles (χ1, χ2) should lead to 3 * 3 = 9 different sidechain orientations according to MDCA. For certain backbone structures, some of the sidechain conformations were nonexistent. © 1996 by John Wiley & Sons, Inc.
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