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.