Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective
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Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective
Accurate description of the intrinsic preferences of amino acids is important to consider when developing a biomolecular force field. In this study, we use a modern energy partitioning approach called Interacting Quantum Atoms to inspect the cause of the φ and ψ torsional preferences of three dipeptides (Gly, Val, and Ile). Repeating energy trends at each of the molecular, functional group, and...
متن کاملRamachandran plot on the web
A graphics package has been developed to display the main chain torsion angles phi, psi (phi, Psi); (Ramachandran angles) in a protein of known structure. In addition, the package calculates the Ramachandran angles at the central residue in the stretch of three amino acids having specified the flanking residue types. The package displays the Ramachandran angles along with a detailed analysis ou...
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متن کاملRedrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints.
A protein backbone has two degrees of conformational freedom per residue, described by its ϕ,ψ-angles. Accordingly, the energy landscape of a blocked peptide unit can be mapped in two dimensions, as shown by Ramachandran, Sasisekharan, and Ramakrishnan almost half a century ago. With atoms approximated as hard spheres, the eponymous Ramachandran plot demonstrated that steric clashes alone elimi...
متن کاملComment on "Revisiting the Ramachandran plot from a new angle".
that the ‘‘forbidden [bridge] region is well-populated in folded proteins, which can provide longer-range intramolecular hydrogen-bond partners.’’ However, using only a hard sphere model, Ramachandran and colleagues predicted the f and c combinations as a function of s that are observed in proteins of known structure. In particular, they showed that f and c combinations in the bridge region are...
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ژورنال
عنوان ژورنال: Journal of Computational Chemistry
سال: 2017
ISSN: 0192-8651
DOI: 10.1002/jcc.24904