Additional examples of WatFinder utility

Here, we present several more case studies on how to use WatFinder.

Case study 1

Detection and quantification of the formation of inter-residue water bridges as adenylate kinase transitions from the closed to open state

IPython notebook (ipynb): caseStudy1

Case study 2

Identification of water influx and clusters into the vesicular monoamine transporter VMAT2

IPython notebook (ipynb): caseStudy2

Case study 3

Identification of key protein-water interactions observed across various Aurora kinase A crystal structures identified by BLAST

IPython notebook (ipynb): caseStudy3

Case study 4

Derection of protein-water interactions that facilitate ligand binding

IPython notebooks (ipynb): caseStudy4a (protein only) and caseStudy4b (protein+ligand)

Case study 5

Water bridges detection in a large chaperonin TRiC/CCT structure including timing for selected regions

IPython notebook (ipynb): caseStudy5

Example 6: WatFinder Parameter Adjustments

IPython notebook (ipynb): watfinder_tab1_1

IPython notebook (ipynb): watfinder_tab1_2

IPython notebook (ipynb): watfinder_tab1_3

IPython notebook (ipynb): watfinder_tab1_4

IPython notebook (ipynb): watfinder_tab1_5

IPython notebook (ipynb): watfinder_tab2_1

IPython notebook (ipynb): watfinder_tab2_2

IPython notebook (ipynb): watfinder_tab2_3

IPython notebook (ipynb): watfinder_tab2_4

The description of all cases are available in the supplementary file of WatFinder paper [JK24]. Trajectories are in tutorial’s files.