MEDock protocols

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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 in pipelines

 (2)
2012
PMCID: 3524943
PMID: 23275691
DOI: 10.6026/97320630008980

[…] from 7 different plants are shown in the (see supplementary material). the top 10 compounds were further docked against aldose reductase using 5 others docking programs gold, patchdock, ehits, medock and autodock vina. the docking scores of the 10 best compounds attained using different software are listed in (see supplementary material). each docking program is listing different compound […]

2012
PMCID: 3524943
PMID: 23275691
DOI: 10.6026/97320630008980

[…] is a widely used approach to improve the scoring reliability and hit rate in virtual screening and four standalone programs (gold, molegro, autodock and e-hits) and two online servers (patchdock and medock) are utilized to rank top hits. allium38 ranked high and reported to be the best compound that can bind with high affinity to aldose reductase enzyme. allium38 resulted in best hits […]


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MEDock in publications

 (4)
PMCID: 4396153
PMID: 25542608
DOI: 10.1186/1742-4682-11-52

[…] evolution processes to search conformations of complex targets and chemical structures, are commonly used in docking protocols, such as autodock []. chang et al. have offered a better alternative, medock []. although medock did not completely exploit entropic-based inductive inference for searching, it does utilize the maximum entropy principle as a guideline to make decisions […]

PMCID: 3602891
PMID: 23519364
DOI: 10.6026/97320630009207

[…] 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 […]

PMCID: 3524943
PMID: 23275691
DOI: 10.6026/97320630008980

[…] calendula officinalis and lycopersicon esculentum) with aldose reductase as the target protein. molecular docking and re-scoring of top ten compounds (using gold, autodock vina, ehits, patchdock and medock) followed by rank-sum technique identified compound allium38 with high binding affinity for aldose reductase., there are several protein targets known to be linked with type 2 diabetes. […]

PMCID: 3355733
PMID: 22645571
DOI: 10.3389/fpls.2012.00017

[…] (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 […]


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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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