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Protocols

LigPrep specifications

Information


Unique identifier OMICS_18799
Name LigPrep
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline QikProp Team

Additional information


A registration is needed to access to tool. Tuto: https://www.schrodinger.com/training/ligprep-workshop-tutorial

LigPrep citations

 (469)
library_books

Evolutionary Analysis Provides Insight Into the Origin and Adaptation of HCV

2018
Front Microbiol
PMCID: 5938362
PMID: 29765366
DOI: 10.3389/fmicb.2018.00854

[…] these observations indicate that the binding interaction pose obtained with the two docking methods is reliable., the c19 sphingomyelin ligand structure was prepared for simulation using the ligprep module of maestro (schrodinger release, 2016-4: maestro schrodinger, llc, new york, ny, united states, 2016) to determine the 3d structure and ionization states at ph 7.0 ± 0.2. the ns5b […]

library_books

Discovery of Natural Products as Novel and Potent FXR Antagonists by Virtual Screening

2018
PMCID: 5936786
PMID: 29761098
DOI: 10.3389/fchem.2018.00140

[…] to soften the nonpolar parts of the receptor. after addition of hydrogen atoms and ionization at a ph range of 5.0-9.0, the three-dimensional structures of compounds in the npd were generated with ligprep v3.3 module. standard precision (sp) and extra precision (xp) approaches of glide (friesner et al., ; halgren et al., ) were respectively adopted to dock the molecules into the binding site […]

library_books

High throughput evaluation of macrocyclization strategies for conformer stabilization

2018
Sci Rep
PMCID: 5920116
PMID: 29700331
DOI: 10.1038/s41598-018-24766-5

[…] then back to 3d. these 3d structures were then inspected to ensure correct stereoisomer states as well as trans amide bonds. these, as well as the linear reference structure, were prepared using ligprep.figure 1, figure  shows the macrocyclic designs restrained to and superimposed onto their crystal bioactive references with conserved atoms highlighted. as is shown in this figure, […]

library_books

Improvement of kynurenine aminotransferase II inhibitors guided by mimicking sulfate esters

2018
PLoS One
PMCID: 5915280
PMID: 29689093
DOI: 10.1371/journal.pone.0196404

[…] the protein preparation wizard in maestro version 10.4.017 (schrodinger llc). the active site was determined by the location of kynurenine in the crystal structure. the ligands were prepared using ligprep [], using the opls-2005 force field, and were docked using glide [] with xp docking []. both enantiomers of ns-1502 and jn-03 were docked, with the best scoring pose represented […]

library_books

Curcumin interacts directly with the Cysteine 259 residue of STAT3 and induces apoptosis in H Ras transformed human mammary epithelial cells

2018
Sci Rep
PMCID: 5913338
PMID: 29686295
DOI: 10.1038/s41598-018-23840-2

[…] from pdb bank. stat3 protein was prepared with neutralization and energy minimization using proteinprep wizard. curcumin was prepared with protonation at ph 7.4 and energy minimization using ligprep module. in a covalent docking module, the reaction type of ligand was set to micheal addition with cysteine 259 of stat3 protein. grid box was generated with residues within 5.0 å […]

library_books

Scaffold hopping from (5 hydroxymethyl) isophthalates to multisubstituted pyrimidines diminishes binding affinity to the C1 domain of protein kinase C

2018
PLoS One
PMCID: 5895059
PMID: 29641588
DOI: 10.1371/journal.pone.0195668

[…] a reference compound in docking. prior to the docking, the target protein was prepared with maestro’s protein preparation tool, and 3d coordinates of the compounds were calculated by schrödinger’s ligprep utilizing epik to generate protonation states. for scoring, we used glide’s “docking score”., all reagents were acquired from sigma-aldrich (schnelldorf, germany), fluorochem (hadfield, […]


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