HADDOCK: a protein-protein docking approach based on biochemical or biophysical information.

By C. Dominguez, Rolf Boelens, Alexandre M. J. J. Bonvin. 2003

3,015 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology, Computational Biology & Bioinformatics, Computational Chemistry & Drug Discovery

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

In Materials Chemistry

In Molecular Biology

In Computational Biology & Bioinformatics

In Computational Chemistry & Drug Discovery

Citations in the corpus

Molecular Docking and Structure-Based Drug Design Strategies (2015, neutral): “score the predicted binding conformations [124].”
Sequence co-evolution gives 3D contacts and structures of protein complexes (2014, methodology): “As a negative control, each protein complex was also docked using center of mass restraints (ab initio docking mode of HADDOCK)38 alone and in the case of the controls generating 10000/500/500 models.”
Information-driven protein–DNA docking using HADDOCK: it is a matter of flexibility (2006, methodology): “Our modelling of protein DNA complexes is based on AIRs to drive the docking process.”
Enhancing structure prediction and design of soluble and membrane proteins with explicit solvent-protein interactions (2017, methodology): “…et al., 2005)), HADDOCK (protein modeling refinement step using physically-based Molecular Dynamics simulations (MD) with explicit solvent (de Vries et al., 2007; Dominguez et al., 2003)) and Modeller (homology modeling technique using knowledge-based implicit solvation (Eswar et al., 2008)).”
The scoring of poses in protein-protein docking: current capabilities and future directions (2013, methodology): “These range from composite scoring functions using a linear combination of terms, usually models of the underlying physical phenomena at play [52-65], to methods derived from the statistics of structural databases [63,66-70], docking decoys [71-75], experimental binding energies [76], methods based ”
High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock (2017, methodology): “For peptide docking within the HADDOCK docking framework [12], the peptide backbone is represented by idealized conformation(s), such as alpha helix, beta strand and polyproline-II, followed by rigid-body, semi-flexible and fully-flexible docking with explicit solvation [18].”
Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis (2017, methodology): “We consider them putative contacts (whether realized or not in the known dimer structures), they are utilized in HADDOCK (37) docking studies to determine whether accurate structural models of homo-dimers can be inferred from sequence derived contact information, cf. Methods for details.”
MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing (2019, background): “pl/pyry3d), and more recently in HADDOCK (Dominguez et al., 2003; RoelTouris et al., 2019), our integrative modeling platform.”
3D RNA and Functional Interactions from Evolutionary Couplings. (2015, positive): “To determine whether EC-derived RNA-protein contacts improve 3D structure prediction of RNAprotein complexes, we used these contacts as restraints for rigid body docking in HADDOCK (Dominguez et al., 2003).”
High-resolution protein complexes from integrating genomic information with molecular simulation (2009, background): “In the Spo0B/Spo0F cocrystal structure contacts are made with this interface that were implied in sealing of the phosphotransfer active site from solvent access (6, 7, 11).”
A protein–DNA docking benchmark (2008, background): “3.pro (11) and dna-rna_allatom.top topology files (12) naming for direct use in HADDOCK (13).”
Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds (2016, neutral): “To demonstrate this diﬀerence we considered calculating the structure of the E2A-HPR complex [22] using a set of ambiguous interaction restraints (AIRs), based on NMR titration data [21].”