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. 2007 Dec 1;69(4):726-33.
doi: 10.1002/prot.21723.

HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets

Sjoerd J de Vries  1 , Aalt D J van Dijk, Mickaël Krzeminski, Mark van Dijk, Aurelien Thureau, Victor Hsu, Tsjerk Wassenaar, Alexandre M J J Bonvin
Affiliations

HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets

Sjoerd J de Vries et al. Proteins. .

Abstract

Here we present version 2.0 of HADDOCK, which incorporates considerable improvements and new features. HADDOCK is now able to model not only protein-protein complexes but also other kinds of biomolecular complexes and multi-component (N > 2) systems. In the absence of any experimental and/or predicted information to drive the docking, HADDOCK now offers two additional ab initio docking modes based on either random patch definition or center-of-mass restraints. The docking protocol has been considerably improved, supporting among other solvated docking, automatic definition of semi-flexible regions, and inclusion of a desolvation energy term in the scoring scheme. The performance of HADDOCK2.0 is evaluated on the targets of rounds 4-11, run in a semi-automated mode using the original information we used in our CAPRI submissions. This enables a direct assessment of the progress made since the previous versions. Although HADDOCK performed very well in CAPRI (65% and 71% success rates, overall and for unbound targets only, respectively), a substantial improvement was achieved with HADDOCK2.0.

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