Mark Hallen

According to our database, Mark Hallen authored at least 9 papers between 2011 and 2019.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2019

Protein design by provable algorithms.

Mark A. Hallen, Bruce Randall Donald

Commun. ACM, 2019

2018

OSPREY 3.0: Open-source protein redesign for you, with powerful new features.

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

J. Comput. Chem., 2018

Protein Design by Algorithm.

Mark A. Hallen, Bruce Randall Donald

CoRR, 2018

2017

LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency.

Mark A. Hallen, Jonathan D. Jou, Bruce Randall Donald

J. Comput. Biol., 2017

CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions.

Mark A. Hallen, Bruce Randall Donald

Bioinform., 2017

2016

cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design.

Yuchao Pan, Yuxi Dong, Jingtian Zhou, Mark Hallen, Bruce Randall Donald, Jianyang Zeng, Wei Xu

J. Comput. Biol., 2016

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.

Mark A. Hallen, Bruce Randall Donald

J. Comput. Biol., 2016

2015

Comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence.

Mark Hallen, Bruce Randall Donald

Proceedings of the Research in Computational Molecular Biology, 2015

2011

Computation of Steady-State Probability Distributions in Stochastic Models of Cellular Networks.

Mark Hallen, Bochong Li, Yu Tanouchi, Cheemeng Tan, Mike West, Lingchong You

PLoS Comput. Biol., 2011