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Dockovalent specifications

Information


Unique identifier OMICS_13716
Name Dockovalent
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Jack Taunton <>

Publication for Dockovalent

Dockovalent in publications

 (3)
PMCID: 5385555
PMID: 28393888
DOI: 10.1038/srep46188

[…] of the informatics methods used to solve the enzymes structure are given in ., a model est6-wt was built from the 97% identical structure of est6-1 using foldx. covalent docking was performed with dockovalent, a covalent version of dock3.7. the program pre-generates a set of conformations for each ligand, covalently attaches the ligand to a receptor, and exhaustively samples ligand […]

PMCID: 5381946
PMID: 28380040
DOI: 10.1371/journal.ppat.1006289

[…] equilibrated stage of the md trajectories (from 35 to 40 ns) and subsequently optimized with steepest descents for 200 steps. the minimized average structure was then used for the covalent docking., dockovalent [] is a covalent adaptation of dock3.6 [,]. given a pre-generated set of ligand conformation and a covalent attachment point, it exhaustively samples ligand conformations around […]

PMCID: 4303301
PMID: 25513739
DOI: 10.1021/bi501140k

[…] of the new covalent bond, are poorly modeled by the noncovalent terms of standard docking., we were thus inspired to investigate the application of a new covalent docking screening method, dockovalent, to substrate prediction for enzymes that proceed through covalent intermediates. the method combines covalent bond-length and angle constraints with noncovalent complementarity, drawn […]


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Dockovalent institution(s)
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA, USA; Faculty of Pharmacy & Ontario Institute for Cancer Research, University of Toronto, Toronto, Canada; Clermont Université, UMR 1071 Inserm/Université d’Auvergne, Clermont-Ferrand, France; INRA, USC 2018, Clermont-Ferrand, France; Service de Bactériologie, Centre Hospitalier Universitaire, Clermont-Ferrand, France
Dockovalent funding source(s)
This work was supported by US NIH grant GM59957, by NIH GM71896, by the Ministère de la Recherche et de la Technologie, the Institut national de la santé et de la recherche médicale (UMR Inserm U1071), the Institut National de la Recherche Agronomique (USC-2018), and the Centre Hospitalier Régional Universitaire de Clermont-Ferrand, France. It was also partly supported by an EMBO long term fellowship (ALTF 1121-2011) and the UCSF Program for Breakthrough Biomedical Research, which is funded in part by the Sandler Foundation, by a fellowship from California TRDRP (#19FT-0091), and by Howard Hughes Medical Institute Predoctoral Fellowhip.

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