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2010 – 2019
- 2019
[j7]Mark A. Hallen, Bruce Randall Donald:
Protein design by provable algorithms. Commun. ACM 62(10): 76-84 (2019)- 2018
- [j6]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) - [i1]Mark A. Hallen, Bruce Randall Donald:
Protein Design by Algorithm. CoRR abs/1806.06064 (2018) - 2017
- [j5]Mark A. Hallen, Bruce Randall Donald:
CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions. Bioinform. 33(14): i5-i12 (2017) - [j4]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) - 2016
- [j3]Mark A. Hallen, Bruce Randall Donald:
comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Protein Design Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence. J. Comput. Biol. 23(5): 311-321 (2016) - [j2]Yuchao Pan, Yuxi Dong, Jingtian Zhou, Mark Hallen, Bruce Randall Donald, Jianyang Zeng, Wei Xu:
cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design. J. Comput. Biol. 23(9): 737-749 (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]Mark Hallen, Bruce Randall Donald:
Comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence. RECOMB 2015: 122-135 - 2011
- [j1]Mark Hallen, Bochong Li, Yu Tanouchi, Cheemeng Tan, Mike West, Lingchong You:
Computation of Steady-State Probability Distributions in Stochastic Models of Cellular Networks. PLoS Comput. Biol. 7(10) (2011)
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