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. 2008 Nov 1;95(9):4217-27.
doi: 10.1529/biophysj.108.135814. Epub 2008 Aug 1.

DARS (Decoys As the Reference State) potentials for protein-protein docking

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DARS (Decoys As the Reference State) potentials for protein-protein docking

Gwo-Yu Chuang et al. Biophys J. .

Abstract

Decoys As the Reference State (DARS) is a simple and natural approach to the construction of structure-based intermolecular potentials. The idea is generating a large set of docked conformations with good shape complementarity but without accounting for atom types, and using the frequency of interactions extracted from these decoys as the reference state. In principle, the resulting potential is ideal for finding near-native conformations among structures obtained by docking, and can be combined with other energy terms to be used directly in docking calculations. We investigated the performance of various DARS versions for docking enzyme-inhibitor, antigen-antibody, and other type of complexes. For enzyme-inhibitor pairs, DARS provides both excellent discrimination and docking results, even with very small decoy sets. For antigen-antibody complexes, DARS is slightly better than a number of interaction potentials tested, but results are worse than for enzyme-inhibitor complexes. With a few exceptions, the DARS docking results are also good for the other complexes, despite poor discrimination, and we show that the latter is not a correct test for docking accuracy. The analysis of interactions in antigen-antibody pairs reveals that, in constructing pairwise potentials for such complexes, one should account for the asymmetry of hydrophobic patches on the two sides of the interface. Similar asymmetry does occur in the few other complexes with poor DARS docking results.

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Figures

FIGURE 1
FIGURE 1
Cumulative distributions of the ROC AUC values for the discrimination of near-native structures of enzyme-inhibitor complexes.
FIGURE 2
FIGURE 2
Cumulative distributions of the ROC AUC values for the discrimination of near-native structures of antigen-antibody complexes.
FIGURE 3
FIGURE 3
Cumulative distributions of the ROC AUC values for the discrimination of near-native structures of other complexes.
FIGURE 4
FIGURE 4
Patches of maximum hydrophobicity in antigen-antibody complexes. (a) Hyhel-5 Fab antibody fragment in complex with chicken lysozyme (PDB code 1BQL). (b) Monoclonal antibody Fab D44.1 in complex with chicken lysozyme (PDB code 1MLC). In both panels the antibody fragment is shown as the white solid model, with teal patches representing the regions with maximum hydrophobicity. The lysozyme is shown as a brown cartoon, with light brown patches as regions of maximum hydrophobicity. In both figures the antibody CDRs are oriented upward, showing that the CDR regions include strongly hydrophobic patches, but these do not interact with regions of maximum hydrophobicity on the lysozyme.

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