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Cited by 556

The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

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

Open access
de Vries, Sjoerd J., van Dijk, Aalt D. J., Krzeminski, Mickaël, van Dijk, Mark, Thureau, Aurelien, Hsu, Victor, Wassenaar, Tsjerk, Bonvin, Alexandre M. J. J.·2007·Proteins: Structure, Function, and Bioinformatics
DOI 10.1002/prot.21723
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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. Proteins 2007. © 2007 Wiley‐Liss, Inc.

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Research works printed but not linked: 40

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Metadata

Authors
de Vries, S. J., van Dijk, A. D. J., Krzeminski, M., van Dijk, M., Thureau, A., Hsu, V., Wassenaar, T., & Bonvin, A. M. J. J.
Venue
Proteins: Structure, Function, and Bioinformatics
Publisher
Wiley
Published
2007-10-31
Volume
69
Issue
4
Pages
726-733
ISSN
  • 0887-3585 (ISSN-L)
  • 1097-0134
DOI
10.1002/prot.21723
OpenAlex
W2030728145
Cited by
556
References
3
FWCI
11.37
Type
journal article
Language
en
Open access
green
Licence
onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Funders
  • Netherlands Organization for Scientific Research (700.56.442)
  • European Community (LSHG-CT-2005-018988)
  • FP6 STREP “BacAbs” (LSHB-CT-2006-037325)
  • Integrated Project SPINE2-COMPLEX (031220)

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