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Replication Data for: A Critical Analysis of Computational Protein Design with Sparse Residue Interaction Graphs

Harvard Dataverse (Africa Rice Center, Bioversity International, CCAFS, CIAT, IFPRI, IRRI and WorldFish)

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Title Replication Data for: A Critical Analysis of Computational Protein Design with Sparse Residue Interaction Graphs
 
Identifier https://doi.org/10.7910/DVN/6C6IWA
 
Creator Jain, Swati
Jou, Jonathan
Georgiev, Ivelin
Donald, Bruce
 
Publisher Harvard Dataverse
 
Description The following contains the data and results used in the following paper:

Swati Jain, Jonathan D. Jou, Ivelin S. Georgiev, and Bruce R. Donald. A Critical Analysis of Computational Protein Design with Sparse Residue Interaction Graphs. PLoS Comp Biol. 2017, In press.

To test the hypothesis and results of sparse residue interaction graphs as presented in this manuscript, the archived version of the code can be found at: https://github.com/donaldlab/OSPREY_SparseAStar .

For new empirical designs, we recommend using the latest version of OSPREY 2.1 available at http://www.cs.duke.edu/donaldlab/osprey.php that includes continuous sidechain and backbone flexibility, ensemble-based design, and new and faster methods to calculate energy functions.
 
Subject Chemistry
Computer and Information Science
Other
protein design
Sparse Residue Interaction Graph
A* Search
Distance and Energy Cutoffs
GMEC
OSPREY
 
Language English
 
Contributor Jou, Jonathan
Donald Lab at Duke University
 
Type Program input data and output data