Epik protocols

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Epik specifications

Information


Unique identifier OMICS_16063
Name Epik
Software type Package/Module
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Maintained Yes

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Maintainer


  • person_outline John Shelley <>

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Publications for Epik

Epik in pipelines

 (2)
2017
PMCID: 5500575
PMID: 28684785
DOI: 10.1038/s41598-017-05058-w

[…] 9. the screening database, emolecules plus, was prepared with ligprep to desalt, add hydrogen atoms and generate tautomers, stereoisomers (max 32) and 3d conformations (max 10 ring conformations). epik and the opls 2005 force field were applied to generate charge states at ph: 7.0 ± 1.0. ligfilter was used to remove structures with reactive functional groups and match the properties […]

2014
PMCID: 4263601
PMID: 25501935
DOI: 10.1371/journal.pone.0114131

[…] and used in the subsequent docking studies., the ligands bosutinib, dasatinib, dorsomorphin, and ly-364947 were processed with ligprep . the processing ensured proper bond orders and, using the epik , module, generated all possible tautomers of the ligands to reflect a ph in the range of 5.0 to 9.0. sitemap , software was used to probe the surface of the tβr-1 for possible binding […]


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Epik in publications

 (20)
PMCID: 5884943
PMID: 29651242
DOI: 10.3389/fphar.2018.00277

[…] ca). then ligprep (version 2.4, schrödinger, llc, new york, ny, 2010) was used to generate stereoisomers and tautomers, and the protonation states of ligands at ph 7.0 ± 2.0 were generated with epik (shelley et al., ). for other parameters, the default values were assigned., currently, there are 10 available x-ray crystal structures of ido1 complexed with different inhibitors in the protein […]

PMCID: 5791933
PMID: 27967218
DOI: 10.1089/ars.2016.6897

[…] atoms was performed using opls3. the bsh structure was obtained from pubchem (id: cid 42614123) and processed with the ligand preparation wizard. the ligand was protonated at ph of 7.0 ± 2.0 using epik (). covalent molecular docking was performed using covdock (), which combines the two programs glide () for docking and prime (, ) for minimization. cysteine 151 was set as reactive residue, […]

PMCID: 5817085
PMID: 29492402
DOI: 10.3389/fchem.2018.00023

[…] fit docking, and pharmacophore generation. the validated compounds were then used for further studies., blind docking using sp and xp was done without specifying the active site residues. the epik state penalties were added to the docking score (shelley et al., ; greenwood et al., ). scaling of van der waals radii was also set to 0.8 and partial charge cutoff at 0.15. the number of poses […]

PMCID: 5855675
PMID: 29401640
DOI: 10.3390/ijms19020453

[…] this set of ligands was prepared with the ligprep tool implemented in maestro, using the opls2005 force field [], and all possible ionization states and tautomers at ph 7 ± 1 were generated with epik [,]. through this procedure, we obtained a total of 146 ligands that were subsequently split into two groups according to the reported mic values. specifically, we considered active compounds […]

PMCID: 5684135
PMID: 29133784
DOI: 10.1038/s41467-017-01508-1

[…] maestro software. the ligprep module in schrodinger software was introduced for geometric optimization by using opls_2005 force field. the ionization states of ligands were calculated with epik tool employing hammett and taft methods in conjunction with ionization and tautomerization tools., the docking of a ligand to the receptor was performed using glide. cubic boxes centered […]


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Epik institution(s)
Schrödinger Inc, New York, NY, USA

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