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