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rDock specifications

Information


Unique identifier OMICS_03835
Name rDock
Alternative name RiboDock
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Xavier Barril <>
  • person_outline Roderick Hubbard <>
  • person_outline David Morley <>

Publications for rDock

rDock in publications

 (50)
PMCID: 5833004
PMID: 29532017
DOI: 10.1021/acscentsci.7b00401

[…] supporting information). multiple crystal structures were used because of the flexibility of the arg1173 side chain and the rigid-protein protocol employed for docking by the open-source software rdock. the acetyl benzene was initially oriented in the binding site to mimic the kac residue as observed in the crystal structure and then underwent flexible docking. the poses obtained by docking […]

PMCID: 5744107
PMID: 29186022
DOI: 10.3390/toxins9120387

[…] and electrostatic energy) clusters that included the most structures for both resting and activated complexes. the poses from the three clusters with high zdock scores were selected and minimized by rdock. to determine which pose was more stable, the interaction energies were calculated, and then the most favorable binding mode was gained. docking data indicated that in mnav1.7, the residues […]

PMCID: 5767197
PMID: 29134431
DOI: 10.1007/s10822-017-0083-9

[…] conformation displayed in pdb id 3oki, and putative binding modes for the entire series were manually created from the binding mode of compound 83., all docking calculations were performed with rdock, generating the cavity using the two-sphere method available in the program, centering a 15 å cavity within residues m294, i356, s336 and y373 using 1.5 and 4.0 å for the radius of the small […]

PMCID: 5556075
PMID: 28808284
DOI: 10.1038/s41598-017-08747-8

[…] as previous computational reports, , , , , ., evolution of size and shape of the ap and dp during the md simulations was examined using the two-probe sphere method of rbcavity program bundled in the rdock suite. this allows obtaining detailed information on the pocket volume and plasticity of the site. in this method, the binding site volume was identified by a fast grid-based cavity detection […]

PMCID: 5534670
PMID: 28824609
DOI: 10.3389/fimmu.2017.00834

[…] inc.). the best pose of these two molecules was subsequently docked into gp120 using patch dock server. the shortlisted poses from patchdock and zdock were further refined using fire dock and rdock, respectively., structurally, dc-sign is composed of an extracellular domain (ecd) which exists as a tetramer, stabilized by an n-terminal α-helical neck region, followed by a crd. dc-sign […]


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rDock institution(s)
Departament de Fisicoquimica, Facultat de Farmacia, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain; Vernalis (R&D) Ltd, Granta Park, Cambridge, UK; Amper Programas, Madrid, Spain; Omixon Biocomputing, Budapest, Hungary; Discngine, Paris, France; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain; YSBL, University of York, Heslington, York, UK; Enspiral Discovery Limited, Cambridge, UK; Ariana Pharma, Paris, France
rDock funding source(s)
Supported by the Wellcome Trust (C2D2 initiative; York U.) and the Spanish Ministerio de Economıa y Competitividad (SAF2009-08811& SAF2012-33481; Barcelona U.).

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