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A water site (WS) determination and analysis tool running on the VMD platform. WATCLUST also allows direct transfer of the WS information to Autodock program to perform biased docking. It is ideally suited for studies of the solvent structure on protein surfaces and cavities with a wide range of applications, such as i) determination of WS in protein-ligand binding sites and ii) protein-protein interaction surfaces that evidence hydrophilic hot-spots, iii) determination of water structure in water/ion channels and iv) characterization of catalytic waters, among others.
ProBiS H2O
Identifies conserved water sites in proteins. ProBiS H2O (1) collects similar macromolecular systems, (2) performs local/specific binding site superimposition, (3) collects the experimental water location data reported in the parent macromolecule systems, (4) transposes gathered data to the examined system, its specific chain, binding site or individual water, (5) clusters water location data to identify discrete spaces with high conservation of water molecules, and (6) visualizes the data in the context of studied system.
3D-RISM / 3D reference Interaction Site Model
Enables the calculations of thermodynamics, electronic properties and molecular solvation structure of a solute molecule in a given molecular liquid or mixture. 3D-RISM allows users to study chemical reactions, including reaction coordinates and transition state search. Moreover, it supplies all of the solvation thermodynamics, including the solvation free energy potential, its energetic and entropic decomposition, and partial molar volume and compressibility.
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