iGEMDOCK statistics

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Citations per year

Number of citations per year for the bioinformatics software tool iGEMDOCK
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Tool usage distribution map

This map represents all the scientific publications referring to iGEMDOCK per scientific context
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Associated diseases

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Protocols

iGEMDOCK specifications

Information


Unique identifier OMICS_23130
Name iGEMDOCK
Software type Framework/Library
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Stability No
Maintained No

Versioning


No version available

Maintainer


This tool is not available anymore.

Publication for iGEMDOCK

iGEMDOCK citations

 (31)
library_books

Characterization of a novel sugar transporter involved in sugarcane bagasse degradation in Trichoderma reesei

2018
Biotechnol Biofuels
PMCID: 5879799
PMID: 29619080
DOI: 10.1186/s13068-018-1084-1

[…] of protein biological functions, as it compares the designed models to different libraries of proteins with previously identified functions [, ].The docking analysis was performed using the software iGEMDOCK v. 2.1, a Generic Evolutionary Method for molecular DOCKing, developed by Jinn-Moon Yang (http://gemdock.life.nctu.edu.tw/dock/igemdock.php). It computes the interaction between one or more l […]

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Synthesis, characterization, computational studies and biological activity evaluation of Cu, Fe, Co and Zn complexes with 2 butanone thiosemicarbazone and 1,10 phenanthroline ligands as anticancer and antibacterial agents

2018
PMCID: 5938540
PMID: 29743867
DOI: 10.17179/excli2017-984
call_split See protocol

[…] Computational studies were performed using computer aided softwares. Molecular docking was done using iGEMDOCK version 2.0 and OSIRIS data warrior version 4.6.1 was used to assess toxicity whereas Molinspiration version 2016.03 was used to calculated bioactivity score and other physicochemical propert […]

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Investigation and identification of functional post translational modification sites associated with drug binding and protein protein interactions

2017
BMC Syst Biol
PMCID: 5763307
PMID: 29322920
DOI: 10.1186/s12918-017-0506-1
call_split See protocol

[…] cate hydrogen bonds, salt bridges, and metal interactions. Green solid lines show hydrophobic interactions and green dashed lines represent π-π and π-cation interactions.In step 2, a docking program, iGEMDOCK 2.0 [], was utilized for the computational extraction of drug binding sites. We followed the four sequential steps in iGEMDOCK to perform the drug-target interaction analysis: target and data […]

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Phytochemical analysis and docking study of compounds present in a polyherbal preparation used in the treatment of dermatophytosis

2017
PMCID: 5917095
PMID: 29707673
DOI: 10.29252/cmm.3.4.6
call_split See protocol

[…] of these compounds were obtained from Pubchem database. The SDF files were converted into PDB file format using OPEN BABEL software. Protein-ligand docking The initial rough docking was performed in iGEMDOCK software (version 2.0) with a population size of 150 and 70 generations, set as default. Protein-ligand docking was carried out in Autodock Vina [], which is an interactive molecular graphics […]

library_books

Structural Insights into the Cytotoxic Mechanism of Vibrio parahaemolyticus PirAvp and PirBvp Toxins

2017
Mar Drugs
PMCID: 5742833
PMID: 29194352
DOI: 10.3390/md15120373

[…] pounds can be virtually docked into specific sites on PirAvp or PirBvp. Furthermore, the binding affinities between PirAvp/PirBvp and compounds can be predicted using molecular docking tools, such as iGEMDOCK [] and AutoDock Vina []. Ligand-based screening is another approach that can be used to identify inhibitors []. On the assumption that similar compounds can mimic physicochemical properties o […]

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Molecular Simulation based Combinatorial Modeling and Antioxidant Activities of Zingiberaceae Family Rhizomes

2017
PMCID: 5669121
PMID: 29142438
DOI: 10.4103/pm.pm_82_17
call_split See protocol

[…] he protein–ligand interactions. Docking allows virtually screening compounds and predicting the strongest binders based on their scoring functions. The software used here to do docking simulation was iGEMDOCK against all prepared compounds. This system's total energy alias Gibbs energy (kcal/mol) is calculated and recorded by the system. […]


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iGEMDOCK institution(s)
Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan; Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan; Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan
iGEMDOCK funding source(s)
Supported by National Science Council and partial support of the ATU plan by MOE.

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