Udock specifications

Information


Unique identifier OMICS_17335
Name Udock
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Computer skills Medium
Stability Alpha
Maintained Yes

Versioning


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Maintainer


  • person_outline Guillaume Levieux <>

Additional information


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Publication for Udock

Udock in publications

 (5)
PMCID: 5524728
PMID: 28790989
DOI: 10.3389/fmicb.2017.01383

[…] in moe. the default settings in asedock2005 were applied to search for the candidate docking structures, and the structures with the best docking score expressed by the arbitrary docking energy (udock) in asedock2005 were selected for the analysis of the protease-substrate interaction sites., chemical compounds that have some structural similarity with the cleavage site of the fcv f4 strain […]

PMCID: 5614712
PMID: 28955773
DOI: 10.1016/j.bbrep.2017.07.002

[…] the ligand-binding sites were defined by the site finder application in moe and docking simulations were carried out using asedock . the lowest energy conformations with the smallest energies (udock and utotal values) were obtained nine times. the utotal and udock values were utilized for the evaluation of the protein-ligand interaction. utotal (kcal/mol) is the sum of uele (electrostatic […]

PMCID: 3530883
PMID: 23275711
DOI: 10.6026/97320630081147

[…] the 200 poses with the lowest utotal values were selected for further optimization with the mmf94s force field. during the refinement step, the ligand was free to move within the binding pocket. udock values were also adopted to determine the most reasonably docked gahmgb1- dna complex., the sequence alignment of hmgb1 (pdb code: 2gzk) and the duplex containing the consensus sequence […]

PMCID: 3433708
PMID: 22973264
DOI: 10.3389/fmicb.2012.00312

[…] et al., ). default setting in asedock2005 was applied for the search of the candidate docking structures, and the structures with the best docking score expressed by the arbitrary docking energy (udock) in asedock2005 (kataoka and goto, ) were selected for the analysis of the protease-substrate interaction sites., the amino acid diversity at individual sites of the sav protease domain […]

PMCID: 3102706
PMID: 21637809
DOI: 10.1371/journal.ppat.1002068

[…] thr151, affecting orientation of the 130-loop (). therefore, the double 129δ/i151t mutation might affect the contact angle between human-type receptor ligands and viral ha., in our simulation, the udock scores of the complexes between the saα2,6 human-type receptor ligand and eg/d1, eg/d1q192h and eg/d1129δ,i151t ha were −13.51, −18.05 and −16.48 kcal/mol, respectively (). therefore, the udock […]


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Udock institution(s)
Equipe Interactivité pour Lire et Jouer, Laboratoire CEDRIC, Conservatoire National des Arts et Métiers, Paris, France; Laboratoire Génomique Bioinformatique et Applications, Conservatoire National des Arts et Métiers, Paris, France

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