Scipion-EM-ProDy

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• Introduction
  • Required Programs
  • Installation
  • Getting Started in Scipion
• Core calculations: select, ANM, deformation and comparison
  • Getting started
  • First workflow from 2 protocols: importing and selecting
  • Another way of parsing and selecting
  • Step 2: dynamics calculations - NMA and deformation vector analysis
  • Step 3: analysis
• Ensemble analysis: dynamics from PCA of multiple structures.
  • Getting started
  • Simple case, steps 0 and 2-i: importing related structures and building an ensemble
  • Advanced case: many heterogeneous structures
  • Step 2-ii: PCA
  • Step 3: analysis 1 - compare modes
  • Step 3: analysis 2 - project ensembles on PCA landscapes

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”.