WatFinder - water bridges within protein structure detector

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Tutorial files: ZIP TGZ

• Introduction
  • Required Programs
  • Recommended Programs
  • Getting Started
• 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”.