## Expected network degree for move set MS1

The set of programs described in the articleare available here: MS1 code

- Clote P. Expected degree of RNA secondary structure networks. J Comput Chem. 2015 Jan 15;36(2):103-17. doi: 10.1002/jcc.23776. Epub 2014 Nov 7

These programs compute the
expected network degree (expected number of neighbors) for the directed
graph ` G = (V,E) `, where V is the set of all secondary structures
of a given RNA sequence, and E is the set of directed edges
s → t, where structure t is obtained from s by an element of move
set MS1 consisting of base pair additions and removals.

## Expected network degree for move set MS2

The set of programs described in the articleare available here: MS2 code

- P. Clote, A. Bayegan. Network properties of the ensemble of RNA structures. submitted, 25 June 2015.

These programs compute the
expected network degree (expected number of neighbors) for the directed
graph ` G = (V,E) `, where V is the set of all secondary structures
of a given RNA sequence, and E is the set of directed edges
s → t, where structure t is obtained from s by an element of move
set MS2 consisting of base pair additions, removals, and shifts,
The algorithm is not a simple extension of the algorithm for MS1, but
requires entirely new concepts and is surprisingly complex.

## Some data and Python code

Here is the data used (from both PDB and Rfam), along with code to compute contact order, and to approximate the distribution of network degree by sampling: