Table 1.

List of available software to predict water molecules’ positions and orientation.

Software	Testing set	Accuracy*	Remarks
Docking-based
Dowser[30]	14 crystal structures of OppA; D- and K-channels of cytochrome c oxidase; Photosystem II	63%	Not available
Dowser+[31]		74%	Not available
Dowser++ [39]		85%	Dowser++ standalone link
WaterDock [32]	14 crystal structures of OppA; HIV-1 protease; ribonuclease A; GluR2 ligand binding core; concanavalin A; glutathione S-transferase; carbonic anhydrase	88%	the code is available with the WaterDock 2.0 Pymol plugin: – link
WaterDock 2.0 [47]	14 crystal structures of OppA; HIV-1 protease; GluR2 ligand binding core; bovine pancreatic trypsin; glutathione S-transferase; HSP90; PIM1; series of 184 BRD4-BD1 complexes; androgen receptor; casein kinase II; thrombin; carbonic anhydrase	91%	WaterDock 2.0 standalone link WaterDock 2.0 Pymol plugin link
RISM-based
3D-RISM[33]	Alanine dipeptide; HIV-1 protease	–	Not available
GAsol [34]	HIV-1 protease; neuraminidase; bovine pancreatic trypsin; series of 184 BRD4-BD1 complexes	94.3%	BSD 3-clause license link
Placevent [35]	HIV-1 protease; rotor ring of F-ATP synthase	water position error ~0.5 Å	the code and tutorial link
Similarity-based
ProBis H2O [37]	Src kinase with bound bosutinib; human programmed death 1 (hPD) with ligand (hPD-L1); DNA Gyrase B; human matrix metalloproteinase (hMMP-1)	–	GUI – PyMOL integrated link
PyWATER [36]	thrombin; trypsin; BPTI; bromodomain-containing protein 4; MHC class I proteins; class A β-lactamases	identified all crystallographic water molecules	GUI – PyMOL integrated link

*Accuracy was calculated based on the number and quality of identified crystallographic water molecules. The numbers were taken from original publications. Please note that there are some differences in the details of the accuracy measurements. Information about currently unavailable software is in italics.