WaterMap specifications


Unique identifier OMICS_18861
Name WaterMap
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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WaterMap in publications

PMCID: 5734604
PMID: 29111736
DOI: 10.1021/acs.jmedchem.7b00861

[…] structure of taranabant bound to hcb1 (pdb 5u09) because both compounds share a trifluoromethylpyridine moiety on their “right arm”., using the crystal structure of the hcb1–29 complex, we performed watermap calculations to try and understand the differences in residence times observed for the ligands studied, with the hypothesis that unfavorable hydration might provide an explanation.− […]

PMCID: 5656095
PMID: 29094109
DOI: 10.1016/j.chempr.2017.07.009

[…] cleft of the crystalized ptpa (d), we performed md simulations coupled with statistical thermodynamic analysis to assess the location and energetics of structural waters. we used the program watermap,, which combines a short (2 ns) md simulation with solvent clustering and thermodynamic analysis by using inhomogeneous solvation theory., this approach has been used to characterize […]

PMCID: 5601358
PMID: 28806076
DOI: 10.1021/acs.jmedchem.7b00950

[…] we decided to further investigate the ligand–receptor interactions using a homology model of the adenosine a3 receptor, based on the crystal structure of the adenosine a2a receptor (pdb 4eiy). watermap calculations were applied to try and explain the variance in kinetic profiles of different ligands by unfavorable hydration.,, antagonist 2 (in black stick representation) was docked […]

PMCID: 5431542
PMID: 28484248
DOI: 10.1038/s41598-017-01491-z

[…] hydration of the atp binding site across several kinases and suggested that the differences could be exploited to improve potency and selectivity of kinase inhibitors. a computational method called watermap later rationalized the differing affinities of a range of kinase inhibitors based on differences in atp site hydration. in a more recent exhaustive study, nicholas and steven reported […]

PMCID: 5331458
PMID: 28079371
DOI: 10.1021/acs.jcim.6b00483

[…] mode flips. they captured the thermodynamic behavior of the different ligands and binding poses by performing docking studies and analyzing solvent molecules around the protein using szmap and watermap. the thermodynamic interpretation originally presented is not unambiguous. it was claimed that binding pose d can be explained by the replacement of a “happy” (watermap)/“hydrophilic” […]

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