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Protocols

MEDock specifications

Information


Unique identifier OMICS_17037
Name MEDock
Alternative name Maximum-Entropy based Docking
Interface Web user interface
Restrictions to use None
Input data Ligand, protein
Input format PDBQ, PDB, PQR
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Jung-Hsin Lin

Publication for Maximum-Entropy based Docking

MEDock citations

 (5)
library_books

Docking based inverse virtual screening: methods, applications, and challenges

2018
Biophysics Rep
PMCID: 5860130
PMID: 29577065
DOI: 10.1007/s41048-017-0045-8

[…] this review, the interested reader is recommended to read the original paper (Luo et al. ).Recently, Wang et al. () released another docking-based IVS web server named idTarget. The docking engine is maximum-entropy based docking (MEDock) (Chang et al. ), which was also published as a web server by the same group. AutoDock4RAP (Wang et al. ), an improved version of the scoring function AutoDock4 ( […]

library_books

Mathematical and computational modeling in biology at multiple scales

2014
PMCID: 4396153
PMID: 25542608
DOI: 10.1186/1742-4682-11-52

[…] pletely exploit entropic-based inductive inference for searching, it does utilize the maximum entropy principle as a guideline to make decisions during this process. The fundamental question asked in MEDock is “What is the probability of finding the deepest energy valley in a ligand-target interaction energy landscape?” Maximum entropy provides a direction to update the initial guess of binding mo […]

call_split

A tool for the post data analysis of screened compounds derived from computer aided docking scores

2013
Bioinformation
PMCID: 3602891
PMID: 23519364
DOI: 10.6026/97320630009207
call_split See protocol

[…] rove the probability of identifying ‘true’ ligands []. In our study, we have tested five different scoring functions as used in tools such as: (i) GOLD []; (ii) Patchdock []; (iii) Molegro []; (iv) MEDock []; (v) AutodockVina []. The input for this application is Spread Sheet with an extension of .xls. The spread sheet consists of docking results of various compounds from various docking tools. […]

call_split

Virtual screening of plant derived compounds for aldose reductase inhibition using molecular docking

2012
Bioinformation
PMCID: 3524943
PMID: 23275691
DOI: 10.6026/97320630008980
call_split See protocol

[…] scores to balance errors in single scores and improve the probability of identifying ‘true’ ligands []. In our study, we tested six different scoring functions such as GOLD;Patchdock;eHITS;Molegro;MEDock;Autodock Vina. GOLD;Patchdock;eHITS;Molegro;MEDock;Autodock Vina. […]

library_books

Diversification and Expression of the PIN, AUX/LAX, and ABCB Families of Putative Auxin Transporters in Populus

2012
Front Plant Sci
PMCID: 3355733
PMID: 22645571
DOI: 10.3389/fpls.2012.00017

[…] anual (Wiederstein and Sippl, ). The best model was used for substrate docking. Furthermore, the quality of the protein model was tested using the program ProSA. Substrate docking was performed using MEDOCK. PDB files of all proteins were translated into pdbq files using the PDB2PQR server. For substrate docking prediction, the nucleotide-binding folds (NBFs) were removed. All loops connecting the […]

Citations

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MEDock institution(s)
Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan, China; Graduate Institute of Networking and Multimedia, National Taiwan University, Taipei, Taiwan, China; School of Pharmacy, National Taiwan University, Taipei, Taiwan, China; Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, China
MEDock funding source(s)
Supported by the National Science Council of Taiwan under contract NSC 93-2112-M-002-027.

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