HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets
Publication date
2007-12
Authors
de Vries, S.J.
van Dijk, A.D.J.
Krzeminski, M.N.
van Dijk, M.
Thureau, A.J.M.M.
Hsu, V.
Wassenaar, T.A.
Bonvin, Alexandre M.J.J.
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Document Type
Article
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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.
Keywords
Flexible docking, HADDOCK, Multibody docking, Scoring, docking protein, complex formation, conference paper, methodology, priority journal, protein protein interaction, protein targeting, Taverne
Citation
de Vries, S J, van Dijk, A D J, Krzeminski, M N, van Dijk, M, Thureau, A J M M, Hsu, V, Wassenaar, T A & Bonvin, A M J J 2007, 'HADDOCK versus HADDOCK : New features and performance of HADDOCK2.0 on the CAPRI targets', Proteins: Structure function and bioinformatics, vol. 69, no. 4, pp. 726-733. https://doi.org/10.1002/prot.21723