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A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles

Möglich, Andreas ; Weinfurtner, Daniel ; Maurer, Till ; Gronwald, Wolfram ; Kalbitzer, Hans Robert



Abstract

BACKGROUND: We have developed the program PERMOL for semi-automated homology modeling of proteins. It is based on restrained molecular dynamics using a simulated annealing protocol in torsion angle space. As main restraints defining the optimal local geometry of the structure weighted mean dihedral angles and their standard deviations are used which are calculated with an algorithm described ...

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