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RMSD/log (-value) plots for the FD-/3D () and PD-/3D () methods

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posted on 30.12.2011, 17:33 by Marialuisa Pellegrini-Calace, Janet M. Thornton

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Taken from "Detecting DNA-binding helix–turn–helix structural motifs using sequence and structure information"

Nucleic Acids Research 2005;33(7):2129-2140.

Published online 14 Apr 2005


© The Author 2005. Published by Oxford University Press. All rights reserved

Dark grey dots correspond to HTHxFALSEs and light grey dots to HTHxTRUEs. The solid line limits the critical box used to derive the best threshold line (dashed diagonal line) as described in Materials and Methods. The two pairs of points connected by an arrow correspond to the PDB structures 1LNW (chain A) and 1IXC (chain A), detected as FNs. However, sequences of both entries show MSE instead of the canonical amino acid. The replacement of all MSE with normal Met makes the proteins to be detected as TP (points below arrows).


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