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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 citations

 (4)
library_books

Molecular basis for the behavioral effects of the odorant degrading enzyme Esterase 6 in Drosophila

2017
Sci Rep
PMCID: 5385555
PMID: 28393888
DOI: 10.1038/srep46188

[…] ails 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 orientations […]

library_books

An APE1 inhibitor reveals critical roles of the redox function of APE1 in KSHV replication and pathogenic phenotypes

2017
PLoS Pathog
PMCID: 5381946
PMID: 28380040
DOI: 10.1371/journal.ppat.1006289

[…] 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 the covale […]

library_books

Building a virtual ligand screening pipeline using free software: a survey

2015
Brief Bioinform
PMCID: 4793892
PMID: 26094053
DOI: 10.1093/bib/bbv037

[…] ted conventional screening for non-covalent interactions by dedicated covalent docking methods, e.g. DOCKTITE [] for the MOE package [], CovalentDock [] for AutoDock [, ], CovDock [] for GLIDE [] and DOCKovalent [] for DOCK [, ]. These approaches typically first identify nucleophilic groups in the target protein and electrophilic groups in the ligand and then apply similar search space exploration […]

library_books

Covalent Docking Predicts Substrates for Haloalkanoate Dehalogenase Superfamily Phosphatases

2014
Biochemistry
PMCID: 4303301
PMID: 25513739
DOI: 10.1021/bi501140k

[…] DOCKovalent is a covalent adaptation of DOCK3.6., Given a pregenerated set of ligand conformation and a covalent attachment point, it exhaustively samples ligand conformations around the covalent bond […]

Citations

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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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