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two_layer_paper

The repository of data for the paper titled A kinetic transition network model reveals the diversity of protein dimer formation mechanisms.

There are two folders in the repository, one containing the description of the microstates (/states) and another containing the description of the transition matrices.

The file names follows the {pdbid}_{dissociation entropy} pattern. For example, 1arr_87.0 contains the data for the 1arr PDB structure calculated at $87\ \mathrm{\frac{J}{mol \cdot K}}$.

Microstates

Microstate files contain nine columns:

  • the first column specifies the serial numbers of states
  • the fromA and toA columns specify the start and end points of the native section in the chain A
  • the fromB and toB columns specify the start and end points of the native section in the chain B
  • the inter column specifies the numbers of interchain contacts
  • the weight column specifies the Boltzmann weight of the states
  • the ass column specifies whether the chains are associated
  • the native column specifies whether the microstates belong to the native state

Transition matrices

Transition matrix files contain three columns:

  • the fr column specifies the serial numbers of the tail nodes in the transition graph
  • the to column specifies the serial numbers of the head nodes in the transition graph
  • the w column specifies the weights of directed edges in the transition graph