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Release Notes

v2.5.0 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.

WatFinder - water bridges within protein structure detector¶

You can also read this tutorial in PDF format.

Tutorial files: ZIP TGZ

  • Introduction
    • Required Programs
    • Recommended Programs
    • Getting Started
    • How to Cite
  • Protein Preparation
  • Water bridges detection in a single PDB structure
    • Water bridges prediction
    • Save results in PDB file
    • Access to the raw data
  • Water bridges detection in a trajectory
    • Parse structure with trajectory
    • Save the results
    • Analysis of the results:
    • Information about residues contributing to water bridges
    • Statistical analysis for water bridges
    • Save results as PDB file
  • Water bridges detection in an Ensemble PDB
    • Initial analysis
    • Detecting water centers
  • Finding significant crystallographic waters across heterogeneous X-ray structures
    • Parse multiple PDB structures
    • Protein preparation
    • Aligning all PDB heterogeneous structures onto first PDB
    • Analyzing PDB structures with certain pattern
    • Finding clusters of water within homologous structures
  • Additional examples of WatFinder utility
    • Case study 1
    • Case study 2
    • Case study 3
    • Case study 4
    • Case study 5
    • Example 6: WatFinder Parameter Adjustments
  • Changes in the default parameters

Acknowledgments

Continued development of Protein Dynamics Software ProDy and associated programs is partially supported by the NIH-funded R01 GM139297 entitled “Toward a deeper understanding of allostery and allotargeting by computational approaches”.

© Copyright 2010-2015, University of Pittsburgh. Last updated on Feb 06, 2025. Created using Sphinx 1.3.5.

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