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A virtual pebble game to ensemble average graph rigidity
Title
A virtual pebble game to ensemble average graph rigidity
Author
Jacobs, Donald J., Gonzalez, Luis C., Wang, Hui, Livesay, Dennis R.
Date Created
2015
Subjects--Topical
Probabilities, Proteins
Description
Background: The body-bar Pebble Game (PG) algorithm is commonly used to calculate network rigidity properties in proteins and polymeric materials. To account for fluctuating interactions such as hydrogen bonds, an ensemble of constraint topologies...
Calculating ensemble averaged descriptions of protein rigidity without sampling
Title
Calculating ensemble averaged descriptions of protein rigidity without sampling
Author
Jacobs, Donald J., Gonzalez, Luis C., Wang, Hui, Livesay, Dennis R.
Date Created
2012
Subjects--Topical
Biology, Proteins
Description
Previous works have demonstrated that protein rigidity is related to thermodynamic stability, especially under conditions that favor formation of native structure. Mechanical network rigidity properties of a single conformation are efficiently cal...