Replication Data for: A Critical Analysis of Computational Protein Design with Sparse Residue Interaction Graphs
<|begin_of_text|><|start_header_id|>system<|end_header_id|> You are a research archivist expert in dataset metadata. Answer the question truthfully.  <|eot_id|><|start_header_id|>user<|end_header_id|> Here is the Description of a dataset. 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' . Please return only a json list of at most 3 Keywords corresponding to the Description:.<|eot_id|><|start_header_id|>assistant<|end_header_id|> {"Answer" : ["A* Search","Distance and Energy Cutoffs","GMEC","OSPREY","protein design","Sparse Residue Interaction Graph"]} <|eot_id|>
 Here is the Description of a dataset. 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' . Please return only a json list of at most 3 Keywords corresponding to the 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
A* Search; Distance and Energy Cutoffs; GMEC; OSPREY; protein design; Sparse Residue Interaction Graph