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idock specifications

Information


Unique identifier OMICS_03797
Name idock
Interface Web user interface
Restrictions to use None
Input data A protein, a search space defined by a center and a size in unit Å and a set of compounds to dock.
Input format PDB
Output data The predicted free energy, ligand efficiency, RF-Score, hydrogen bonds, molecular properties, link to substance information and supplier list of the successfully docked compounds and the predicted conformations of the top 1000 hit compounds.
Output format GZIP
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline Hongjian Li
  • person_outline Kwong-Sak Leung
  • person_outline Man-Hon Wong

Information


Unique identifier OMICS_03797
Name idock
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++
License Apache License version 2.0
Computer skills Advanced
Version 2.2.2
Stability Beta

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Publications for idock

idock citations

 (9)
library_books

Econazole nitrate inhibits PI3K activity and promotes apoptosis in lung cancer cells

2017
Sci Rep
PMCID: 5740072
PMID: 29269744
DOI: 10.1038/s41598-017-18178-0

[…] pi3kα is closely associated with tumorigenesis. therefore, pi3kα appears to be an ideal target for drug development. in this study, we utilized free and open-source protein-ligand docking software idock,, binding affinity prediction software rf-score-v3, and molecular visualization tool iview to screen 3167 fda-approved small molecules to identify putative pi3kα inhibitors. among them, […]

library_books

Identification of Clinically Approved Drugs Indacaterol and Canagliflozin for Repurposing to Treat Epidermal Growth Factor Tyrosine Kinase Inhibitor Resistant Lung Cancer

2017
PMCID: 5712561
PMID: 29238696
DOI: 10.3389/fonc.2017.00288

[…] the mutation blocks the binding of egfr tkis to the receptor kinase, thereby abolishing the therapeutic efficacy. in this study, we used our free and open-source protein-ligand docking software idock to screen worldwide approved small-molecule drugs against egfr t790m. the computationally selected drug candidates were evaluated in vitro in resistant non-small cell lung cancer (nsclc) cell […]

library_books

In silico based identification of human α enolase inhibitors to block cancer cell growth metabolically

2017
Drug Des Devel Ther
PMCID: 5695255
PMID: 29180852
DOI: 10.2147/DDDT.S149214

[…] (nhs), eu (ema), japanese (nhi), and canadian (hc) authorities to a total number of 3,167., molecular docking and screening were undertaken using the cuda supported multithreading screening program, idock, in a server hosted by the chinese university of hong kong (http://istar.cse.cuhk.edu.hk/idock/)., a grid box encompassing the amino acid side chains involved in catalytic process, including […]

library_books

A Large and Phylogenetically Diverse Class of Type 1 Opsins Lacking a Canonical Retinal Binding Site

2016
PLoS One
PMCID: 4915679
PMID: 27327432
DOI: 10.1371/journal.pone.0156543

[…] binding pocket was identified which was missing or highly diminished in canonical haloarchaeal opsins (, ). to identify candidate ligands for these novel binding pockets, we used the program idock [] to screen 229,358 natural product ligands against the three structurally modeled orp homologs. an overlap analysis of the results showed that, despite their structural similarity, the three […]

library_books

Adapalene inhibits the activity of cyclin dependent kinase 2 in colorectal carcinoma

2015
PMCID: 4626183
PMID: 26398439
DOI: 10.3892/mmr.2015.4310

[…] be overexpressed in human colorectal cancer; it is responsible for the g1-to-s-phase transition in the cell cycle and its deregulation is a hallmark of cancer. the present study was the first to use idock, a free and open-source protein-ligand docking software developed by our group, to identify potential cdk2 inhibitors from 4,311 us food and drug administration-approved small molecular drugs […]

library_books

Machine‐learning scoring functions to improve structure‐based binding affinity prediction and virtual screening

2015
PMCID: 4832270
PMID: 27110292
DOI: 10.1002/wcms.1225

[…] , rf‐score‐v3 (stand‐alone): http://crcm.marseille.inserm.fr/fileadmin/rf‐score‐3.tgz , rf‐score‐v3 (embedded in a webserver for prospective vs88): http://istar.cse.cuhk.edu.hk/idock , open drug discovery toolkit: https://github.com/oddt/oddt , this section addresses the development of machine‐learning sfs designed to tackle applications for which there are still […]


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idock institution(s)
Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong

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