LigPrep protocols

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LigPrep specifications


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


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LigPrep in pipelines

PMCID: 5430761
PMID: 28432357
DOI: 10.1038/s41598-017-01254-w

[…] wizard. domains were searched using cdsearch. then the active site of the protein was predicted with help of dogsitescorer and schrodinger’s siteprep, . the ligands were obtained from zinc database. ligprep was used to prepare the ligands after having the ligands screened for multiple scaffolds. then the ligands were screened using schrodinger’s htvs. the ligands having docking score below −7 kca […]

PMCID: 5500575
PMID: 28684785
DOI: 10.1038/s41598-017-05058-w

[…] dose-response affinity or activity values (k i, pk i, ec50, pec50, ic50 and pic50), and the highest assay confidence scores: 8 or 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 […]

PMCID: 5148588
PMID: 27936128
DOI: 10.1371/journal.pone.0167763

[…] of srte1 using the schrödinger small-molecule drug discovery suite 2015–2 (schrödinger llc, new york, ny, usa). prior to docking, the lpet and laet ligands were constructed and energy minimized with ligprep and the aqa tripeptide was removed from the crystal structure of the enzyme. the receptor (srte1) was also processed with the protein preparation wizard to add missing side chain atoms […]

PMCID: 5239439
PMID: 27384997
DOI: 10.18632/oncotarget.10341

[…] structure of ptp-meg2 (pdb id: 4ge6) was downloaded from the pdb bank. as a potential inhibitor against ptp-meg2, compound 4a was prepared in silicon via the ligand structure preparation module “ligprep”. docking site was determined by original ligand of ptp-meg2 in its crystal structure., molecular dynamics simulation is a tool used to study the interaction between small molecules […]

PMCID: 5260052
PMID: 28155653
DOI: 10.1186/s12859-016-1379-9

[…] the gqsar model was used to predict the activity of the compounds generated in the library., the ligands with highest predicted activity were selected for docking studies and were prepared using the ligprep utility of schrodinger [, ]. with the help of this, energy minimized 3-d structures of the compounds were generated. the protein ck-1δ used in this study was obtained from protein data bank […]

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LigPrep in publications

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 […]

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 […]

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, […]

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 […]

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 […]

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