QSite specifications


Unique identifier OMICS_18857
Name QSite
Software type Application/Script
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Free trial Yes
Maintained Yes


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QSite in publications

PMCID: 5871790
PMID: 29593210
DOI: 10.1038/s41467-018-03545-w

[…] on psii, respectively. d1-his337 was considered to be protonated., the unrestricted density functional theory (dft) method was employed with the b3lyp functional and lacvp* basis sets, using the qsite program. in the qm region, all the atomic coordinates were fully relaxed. in the mm region, the positions of h atoms were optimized using the opls2005 force field, while the positions of heavy […]

PMCID: 5700162
PMID: 29167463
DOI: 10.1038/s41467-017-01821-9

[…] aaplsy-intermediate complexes were first optimized in opls3 force field, using the refine protein–ligand complex tool. then qm/mm approach in dft-b3lyp method was run to find their minimums, using qsite 6.9 program. finally, the transition state for the addition step is obtained by qm/mm approach in the same method; the transition state searching method is linear synchronous transit […]

PMCID: 5651223
PMID: 29081609
DOI: 10.6026/97320630013301

[…] by the mean value) of individual bands of the scanned blot. β- actin was used to normalize the target and the relative expression was stated as fold ratio., ligand binding sites were predicted using qsite finder (http://www.modelling.leeds.ac.uk/qsitefinder/), surface topology and pocket information were analyzed by thecastp server (http://stsfw.bioengr.uic.edu/castp/calculation). the results […]

PMCID: 5431432
PMID: 28473721
DOI: 10.1038/s41598-017-00822-4

[…] initially docked into a rigid protein using glide. the resulting binding modes of the ligands were then used for the calculation of the partial charges of the ligand by a single-point calculation in qsite treating the ligand with the ab initio (b3pw91/cc-pvtz) and the receptor with mm (opls-2005) level of theory. the partial atomic charges of the ligand molecules were recalculated using […]

PMCID: 5058653
PMID: 27166255
DOI: 10.18632/oncotarget.9179

[…] density functional theory (dft) and the lacvp* basis set, the rest of the target was optimized using the opls-2005 force field. qm/mm calculations were performed by means of the version 5.7 of the qsite software [, ]., all graph values represent means ± sem from three independent experiments with each measured in triplicate. the differences between two groups were analyzed with unpaired […]

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