Words similar to rotamer

Example sentences for: rotamer

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Multiple side chain conformations for residue positions that differ in type between the template and target proteins were generated by exploring all the possibilities in a rotamer library [ 31 ] . The most probable conformations based on the interactions of a given conformation with the local main chain were selected using an all-atom distance dependent conditional probability discriminatory function [ 32 ] .
The backbone conformation is captured in the Ramachandran angles φ, ψ [ 1 ] . The rotamer degrees of freedom fixes the entire side chain.
Side chain conformations are predicted by simply using the most frequently observed rotamer in a database of protein structures [ 30 ] . New conformations are generated by perturbing the existing conformation at an arbitrary residue by one of two methods: ( i ) the torsion values for three residues with identical sequence from a known structure are used to modify the current conformation, similar in spirit to that of Baker and colleagues [ 39 ] ; ( ii ) one of possible 14 torsion (φ/ψ) values derived based on the most frequently occurring torsion values for a given residue in a database of known structures.
Rotamer 4 corresponds to the recently proposed bioactive conformation of Taxol bound to β-tubulin.