Water molecule in protein structure is considered as conserved one if there are water molecules in approximately the same position in independently solved structures of homologous proteins.
Conserved water molecules are detected by wLake program (http://mouse.belozersky.msu.ru/~evgeniy/cgi-bin/wLake/wLake.php). wLake takes superimposed structures on input and detects clusters of closely located water molecules from different member of the superimposition. Default threshold for distance between oxygens of two HOH molecules is set to 1.5Å, clusters that share a considerable number of water molecules are joined. See Aksianov et al.2008 (http://www.ncbi.nlm.nih.gov/pubmed/18763742) for details.
Only those clusters that include at least one water molecule on protein – DNA interface are stored in NPIDB complex. The threshold of the number of waters in detected clusters is set to two.
Conserved water molecules on protein – DNA interface can be considered as significant players in protein – DNA interaction (Ramakrishnan, Rajagopalan, 2012,http://www.ncbi.nlm.nih.gov/pubmed/22872098, Spirakis et al., 2007, http://www.ncbi.nlm.nih.gov/pubmed/17214883, Grischchus, Ferreti, 2001, http://www.ncbi.nlm.nih.gov/pubmed/11495243). If a cluster contains also a water molecule from a structure of single protein (no DNA in PDB file) than this water can be considered as preimmobilized at protein surface and playing a role in DNA recognition.