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cellPACK hands-on

Ludovic Autin

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Graham Johnson

Art Olson

Michel Sanner

Dept. of Structural and COmputational BIOlogy

TSRI

NCBR

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autoPACK / cellPACK

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Recipe Structure

  • bounding box
  • exterior
    • ingredients
  • compartment1
    • surface
      • ingredients
    • interior
      • ingredients
  • compartment2
    • surface
      • ingredients
    • interior
      • ingredients
  • etc...

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Ingredient

Required informations:

  • name
  • proxy representation
  • mesh representation
  • molarity or copy number
  • localisation (surface, interior)

Sources : PDB, EMDB, UniProt, PubMed

To Build an ingredient, diffferent options:

  • manually with a text editor
  • guided with autoPACK plugin
  • use a predefined ingredient

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Proxy

Mesh

Representations

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Surface Ingredient

Principal Vector

Offset Vector

Surface Normal Vector

Align Principal Vector (+Offset) to Surface Normal Vector

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cellPACK generated

model Application

  • Research
    • Fluoresence simulation
    • TEM simulation (TEM simulator)
    • Simulation (atomic, brownian, diffusion dynamics, etc...)
  • OutReach
    • Images, Movies and Interactive App
    • 3D printed Tangible Model

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Simulation Example

  • UCSD Influenza virus molecular dynamics in cellVIEW

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  • NVIDIA Flex prototype

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