Citation Context

...cule from each solvation iteration. All non-bulk water molecules are considered to be contained in cavities. The solvated protein structures from the different iterations are superimposed using CLICK =-=(16,17)-=-. Waters from different iterations are clustered together if they lie within 1.2 Å of each other. A cavity is identified if it contains at least two water molecules. Each cavity contains a set of som...

Citation Context

...cule from each solvation iteration. All non-bulk water molecules are considered to be contained in cavities. The solvated protein structures from the different iterations are superimposed using CLICK =-=(16,17)-=-. Waters from different iterations are clustered together if they lie within 1.2 Å of each other. A cavity is identified if it contains at least two water molecules. Each cavity contains a set of som...

Citation Context

... To establish these relationships one needs to make use of nonsequential and non-topological protein structure matching programs (21–23). Here, we report on a web server that uses the CLICK algorithm =-=(24)-=- to align the 3D structures of any pair of biomolecules, independent of topology. The CLICK algorithm aligns 3D structures by matching cliques of points. Cliques are groupings of representative atoms ...

Citation Context

...cule from each solvation iteration. All non-bulk water molecules are considered to be contained in cavities. The solvated protein structures from the different iterations are superimposed using CLICK =-=(16,17)-=-. Waters from different iterations are clustered together if they lie within 1.2 Å of each other. A cavity is identified if it contains at least two water molecules. Each cavity contains a set of som...