CovDock specifications

Information


Unique identifier OMICS_18681
Name CovDock
Software type Pipeline/Workflow
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Free trial Yes
Maintained Yes

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Maintainer


  • person_outline Edward Harder <>

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Publication for CovDock

CovDock in publications

 (8)
PMCID: 5952258
PMID: 29465985
DOI: 10.1021/acsinfecdis.7b00111

[…] that were consistent with the intermediate 30a–nhoh (data not shown). these findings confirm that rv2466c mediated nitroreduction of 30a occurs within mtb., using the covalent docking protocol covdock, we modeled the pose of mycothiol in the active site of rv2466c assuming a disulfide bond formation between the mycothiol cysteine sulfhydryl and the sulfhydryl of rv2466c c19. this model […]

PMCID: 5791933
PMID: 27967218
DOI: 10.1089/ars.2016.6897

[…] obtained from pubchem (id: cid 42614123) and processed with the ligand preparation wizard. the ligand was protonated at ph of 7.0 ± 2.0 using epik (). covalent molecular docking was performed using covdock (), which combines the two programs glide () for docking and prime (, ) for minimization. cysteine 151 was set as reactive residue, and the reaction type was disulfide formation. all atom […]

PMCID: 5660806
PMID: 29158871
DOI: 10.1155/2017/1420892

[…] tric = 1). covalent docking of vp10/12 and vp10/39 was carried out at the btb domain of keap1 as follows: cys 151 was set as reactive residue and the michael's addition reaction was simulated [] with covdock task of schrodinger© maestro []. mmgbsa rescoring of semiflexible docking at the dc domain and covalent docking at btb was carried out with schrodinger© maestro: the vsgb 2.0 model was used an […]

PMCID: 5608908
PMID: 28935948
DOI: 10.1038/s41598-017-12170-4

[…] supplementary material (figures  and , respectively)., after the identification of ss1 and ss2 as protease inhibitor scaffolds with putative nitrile warheads, we used the covalent docking protocol covdock in order to investigate the specific interactions of representatives from each substructure with cruzipain (pdb: 3iut). we defined cys25, the known nucleophile for other covalent inhibitors, […]

PMCID: 5472749
PMID: 28598431
DOI: 10.1038/ncomms15772

[…] then subjected to another virtual screening specifically designed to identify compounds able to covalently target the active site residue c113. to this aim, a covalent docking approach using the covdock-vs method was exploited. these approaches yielded around one hundred possible pin1 covalent binders that were tested afterwards for cytotoxicity against melanoma a375 cells using the mtt […]


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