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Mogul specifications

Information


Unique identifier OMICS_06369
Name Mogul
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Mogul

Mogul in publications

 (5)
PMCID: 5718880
PMID: 29174494
DOI: 10.1016/j.str.2017.10.009

[…] such as chirality errors and polymer linkage artifacts., the geometry of all non-standard or modified residues of a polymer, small-molecule ligands, and carbohydrate molecules is analyzed with the mogul software (). for each bond length, bond angle, dihedral angle and ring pucker, mogul searches through high-quality, small-molecule crystal structures in the cambridge structural database (csd) […]

PMCID: 5119991
PMID: 27863242
DOI: 10.1016/j.cell.2016.10.046

[…] docked into empty density near eef1a and adjusted in coot using real space refinement with chemical restraints generated using phenix.elbow (). the geometry of didemnin b model was analyzed using mogul, a molecular-geometry library derived from the cambridge structural database (csd) (). some of the restraints generated from phenix.elbow were adjusted to match the median angles and distances […]

PMCID: 4686831
PMID: 26640126
DOI: 10.1038/ncomms9833

[…] respectively. the structure was phased by molecular replacement using pdb id 4nie as search model in phaser. ligand restraints were generated using grade (global phasing, version 1.2.8) and ccdc mogul. coot and phenix.refine were used in alternating cycles of model building and refinement. the quality of the final model was evaluated using molprobity. figures were created using pymol (the […]

PMCID: 3680490
PMID: 23776527
DOI: 10.1371/journal.pone.0065689

[…] water molecules removed as a search model. the protein-ligand structures were manually rebuilt in coot and refined with buster in iterative cycles. ligand restraints were generated with grade and mogul . the positioning of the furan ring in compound 13 was guided using isostar maps calculated using data from the cambridge structural database and from the protein databank respectively. […]

PMCID: 3195755
PMID: 22000512
DOI: 10.1016/j.str.2011.08.006

[…] preferably derived by analysis of accurate small-molecule crystal structures (). at present, such descriptions are not generally available but could be derived for most ligands using a tool such as mogul (). mogul analyzes geometrical parameters (bond lengths, angles, torsions) by mining structures from the cambridge structure database (csd; ) to produce the distribution of each parameter […]


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Mogul institution(s)
Cambridge Crystallographic Data Centre, Cambridge, UK

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