Jonathan D Jou
Title
Cited by
Cited by
Year
BWM*: A novel, provable, ensemble-based dynamic programming algorithm for sparse approximations of computational protein design
JD Jou, S Jain, IS Georgiev, BR Donald
Journal of Computational Biology 23 (6), 413-424, 2016
212016
OSPREY 3.0: Open‐source protein redesign for you, with powerful new features
MA Hallen, JW Martin, A Ojewole, JD Jou, AU Lowegard, MS Frenkel, ...
Journal of computational chemistry 39 (30), 2494-2507, 2018
192018
LUTE (Local unpruned tuple expansion): Accurate continuously flexible protein design with general energy functions and rigid Rotamer-Like efficiency
MA Hallen, JD Jou, BR Donald
Journal of Computational Biology 24 (6), 536-546, 2017
162017
BBK* (Branch and Bound Over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large …
AA Ojewole, JD Jou, VG Fowler, BR Donald
Journal of Computational Biology 25 (7), 726-739, 2018
82018
(Branch and Bound over ): A Provable and Efficient Ensemble-Based Algorithm to Optimize Stability and Binding Affinity over Large Sequence Spaces
AA Ojewole, JD Jou, VG Fowler, BR Donald
International Conference on Research in Computational Molecular Biology, 157-172, 2017
8*2017
Artist identification for renaissance paintings
J Jou, S Agrawal
Technical report, 2011
52011
Computational analysis of energy landscapes reveals dynamic features that contribute to binding of inhibitors to CFTR-associated ligand
GT Holt, JD Jou, NP Gill, AU Lowegard, JW Martin, DR Madden, ...
The Journal of Physical Chemistry B 123 (49), 10441-10455, 2019
42019
Minimization-Aware Recursive (MAR): A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the …
JD Jou, GT Holt, AU Lowegard, BR Donald
International Conference on Research in Computational Molecular Biology, 101-119, 2019
22019
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
AU Lowegard, MS Frenkel, GT Holt, JD Jou, AA Ojewole, BR Donald
PLOS Computational Biology 16 (6), e1007447, 2020
12020
Minimization-Aware Recursive K*: A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape
JD Jou, GT Holt, AU Lowegard, BR Donald
Journal of Computational Biology 27 (4), 550-564, 2020
12020
A critical analysis of computational protein design with sparse residue interaction graphs
S Jain, JD Jou, IS Georgiev, BR Donald
PLoS computational biology 13 (3), e1005346, 2017
12017
Supplementary Information: Minimization-Aware Recursive K (MARK): A Novel, Provable Algorithm that Accelerates Ensemble-based Protein Design and Provably Approximates the …
JD Jou, GT Holt, AU Lowegard, BR Donald
2019
Novel Computational Protein Design Algorithms with Sparse Residue Interaction Graphs, Ensembles, and Mathematical Guarantees, and Their Application to Antibody Design
JD Jou
Duke University, 2018
2018
Algorithmic Advances and Applications from RECOMB 2017
P Dao, YA Kim, D Wojtowicz, TM Przytycka, S Madan, R Sharan, ...
CELL SYSTEMS 5 (3), 176-186, 2017
2017
How we responded to reviewers’ comments: Novel, Provable Algorithms for Efficient Ensemble-Based Computational Protein Design and Their Application to the Redesign of the c-Raf …
AU Lowegard, MS Frenkel, GT Holt, JD Jou, AA Ojewole, BR Donald
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