Additional examples of WatFinder utility

Release Notes

v2.4.1 series come with new and improved sequence, structure, and dynamics analysis features. See release notes for details.

How to Cite

Bakan A, Meireles LM, Bahar I ProDy: Protein Dynamics Inferred from Theory and Experiments
Bioinformatics 2011 27(11):1575-1577.

Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics
Bioinformatics 2014 30(18):2681-2683.

Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I ProDy 2.0: Increased scale and scope after 10 years of protein dynamics modelling with Python
Bioinformatics 2021 37(20):3657-3659.

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 which will be available soon. Trajectories are in tutorial’s files and here.