Primary Citation PubMed: 9783745
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A protein-DNA docking benchmark.
(2008) Nucleic Acids Res 36
PubMed: 18583363 | PubMedCentral: PMC2504314 | DOI: 10.1093/nar/gkn386
The benchmark also contains several structures with special features such as strand breaks (PDB entries 1g9z, 1o3t and 3bam) and flipped out bases in the DNA (PDB entries 1diz, 1emh, 1vas and 7mht).
Publication Year: 2008
Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance.
(2010) Nucleic Acids Res 38
PubMed: 20466807 | PubMedCentral: PMC2943626 | DOI: 10.1093/nar/gkq222
These, for instance, involve enzymes that perform their catalytic function on single nucleotides that are flipped out of the helix into a catalytic pocket of the protein (1emh, 7mht), restriction enzy... es clamping themselves around the DNA (3bam,1rva) or proteins with complex dimerization interfaces (1tro, 1f4k).
Publication Year: 2010
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