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ORCIDJonathan D. Jou
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- affiliation: Duke University, Durham, NC, USA
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2020 – today
- 2020
[j7]Jonathan D. Jou, Graham T. Holt, Anna U. Lowegard
, Bruce Randall Donald:
Minimization-Aware Recursive K*: A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape. J. Comput. Biol. 27(4): 550-564 (2020)- [j6]Anna U. Lowegard, Marcel S. Frenkel, Graham T. Holt, Jonathan D. Jou, Adegoke A. Ojewole, Bruce Randall Donald:
Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD: KRas protein-protein interface. PLoS Comput. Biol. 16(6) (2020)
2010 – 2019
- 2019
- [c4]Jonathan D. Jou, Graham T. Holt, Anna U. Lowegard, Bruce Randall Donald:
Minimization-Aware Recursive K^* K ∗ ( MARK^* MARK ∗ ): A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape. RECOMB 2019: 101-119 - 2018
- [b1]Jonathan D. Jou:
Novel Computational Protein Design Algorithms with Sparse Residue Interaction Graphs, Ensembles, and Mathematical Guarantees, and their Application to Antibody Design. Duke University, Durham, NC, USA, 2018 - [j5]Adegoke A. Ojewole, Jonathan D. Jou, Vance G. Fowler, Bruce Randall Donald:
BBK* (Branch and Bound Over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces. J. Comput. Biol. 25(7): 726-739 (2018) - [j4]Mark A. Hallen, Jeffrey W. Martin, Adegoke A. Ojewole, Jonathan D. Jou, Anna U. Lowegard, Marcel S. Frenkel, Pablo Gainza, Hunter M. Nisonoff, Aditya Mukund, Siyu Wang, Graham T. Holt, David Zhou, Elizabeth Dowd, Bruce Randall Donald:
OSPREY 3.0: Open-source protein redesign for you, with powerful new features. J. Comput. Chem. 39(30): 2494-2507 (2018) - 2017
- [j3]Mark A. Hallen, Jonathan D. Jou, Bruce Randall Donald:
LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency. J. Comput. Biol. 24(6): 536-546 (2017) - [j2]Swati Jain, Jonathan D. Jou, Ivelin S. Georgiev, Bruce Randall Donald:
A critical analysis of computational protein design with sparse residue interaction graphs. PLoS Comput. Biol. 13(3) (2017) - [c3]Adegoke A. Ojewole, Jonathan D. Jou, Vance G. Fowler, Bruce Randall Donald:
BBK* (Branch and Bound over K*): A Provable and Efficient Ensemble-Based Algorithm to Optimize Stability and Binding Affinity over Large Sequence Spaces. RECOMB 2017: 157-172 - 2016
- [j1]Jonathan D. Jou, Swati Jain, Ivelin Georgiev, Bruce Randall Donald:
BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design. J. Comput. Biol. 23(6): 413-424 (2016) - [c2]Mark A. Hallen, Jonathan D. Jou, Bruce Randall Donald:
LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid-rotamer-like Efficiency. RECOMB 2016: 122-136 - 2015
- [c1]Jonathan D. Jou, Swati Jain, Ivelin Georgiev, Bruce Randall Donald:
BWM*: A Novel, Provable, Ensemble-Based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design. RECOMB 2015: 154-166
Coauthor Index
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