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. Author manuscript; available in PMC: 2014 Aug 1.
Published in final edited form as: Proteins. 2013 Apr 22;81(8):1318–1329. doi: 10.1002/prot.24272

Figure 5.

Figure 5

Examples of positive and negative effects of explicit waters on protein sidechain prediction. Crystal structure conformations are shown in grey with thin lines; modeled sidechains are shown in stick representation with carbons colored cyan (explicit water simulations) and magenta (implicit water simulations) and DNA in yellow. (a) A water inserts into the protein-DNA interface, displacing the protein sidechain (grey arrow) and replacing a direct with a water-mediated contact. (b) Hydrogen bonds to explicit waters (green dashed lines) help to correctly orient a protein sidechain.