title: HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets.
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.
authors.affiliation: Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, 3584CH, Utrecht, The Netherlands.
authors.forename: Sjoerd J
authors.initials: SJ
authors.lastname: de Vries
authors.forename: Aalt D J
authors.initials: AD
authors.lastname: van Dijk
authors.forename: Mickaël
authors.initials: M
authors.lastname: Krzeminski
authors.forename: Mark
authors.initials: M
authors.lastname: van Dijk
authors.forename: Aurelien
authors.initials: A
authors.lastname: Thureau
authors.forename: Victor
authors.initials: V
authors.lastname: Hsu
authors.forename: Tsjerk
authors.initials: T
authors.lastname: Wassenaar
authors.forename: Alexandre M J J
authors.initials: AM
authors.lastname: Bonvin
mesh_terms: D000465:Algorithms; D001331:Automation; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D018360:Crystallography, X-Ray / Q000379:methods; D030562:Databases, Protein; D023281:Genomics; D015233:Models, Statistical; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D012984:Software