Water-Sensitive Virtual Screening Approaches and Applications

Taking into account the solvent-accessible surface area and the free energies of transfer for each individual atom, Eisenberg and McLachlan [22] reported a method for calculating the degree of conservation of water molecules in protein stmctures. 

neural networks have been applied for investigating protein hydration sites [92]. 

Water-Sensitive Virtual Screening Approaches and Applications 

Docking a ligand into a protein pocket is a combinatorial problem. Algorithms are designed to cover the space of interactions as exhaustively as possible to avoid 

Finally, there are programs that add water molecules after potential ligand poses are found solely to improve the scoring [114—116]. Only in the first two approaches are the structural predictions influenced directly by the water molecules. Obviously, all three possibilities to include explicit water molecules in docking can modify the score of a ligand in comparison to a mere implicit treatment of solvation and desolvation. In doing so the challenge is to correctly quantify water contributions. 

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