Publications by authors named "Mark Hallen"

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Protein Design by Provable Algorithms.
Mark A Hallen, Bruce R Donald

Commun ACM· October 2019

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PLUG (Pruning of Local Unrealistic Geometries) removes restrictions on biophysical modeling for protein design.
Mark A Hallen

Proteins· January 2019

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OSPREY 3.0: Open-source protein redesign for you, with powerful new features.
Mark A Hallen, Jeffrey W Martin, Adegoke Ojewole, Jonathan D Jou, Anna U Lowegard

J Comput Chem· November 2018

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CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions.
Mark A Hallen, Bruce R Donald

Bioinformatics· July 2017

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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 R Donald

J Comput Biol· June 2017

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cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design.
Yuchao Pan, Yuxi Dong, Jingtian Zhou, Mark Hallen, Bruce R Donald

J Comput Biol· September 2016

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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 R Donald

J Comput Biol· May 2016

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Fast gap-free enumeration of conformations and sequences for protein design.
Kyle E Roberts, Pablo Gainza, Mark A Hallen, Bruce R Donald

Proteins· October 2015

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Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env.
Young Do Kwon, Marie Pancera, Priyamvada Acharya, Ivelin S Georgiev, Emma T Crooks, Mark A Hallen

Nat Struct Mol Biol· July 2015

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Compact Representation of Continuous Energy Surfaces for More Efficient Protein Design.
Mark A Hallen, Pablo Gainza, Bruce R Donald

J Chem Theory Comput· May 2015

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Altered nucleotide-microtubule coupling and increased mechanical output by a kinesin mutant.
Hong-Lei Liu, Mark A Hallen, Sharyn A Endow

PLoS One· March 2013

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Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and backbone flexibility.
Mark A Hallen, Daniel A Keedy, Bruce R Donald

Proteins· January 2013

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Computation of steady-state probability distributions in stochastic models of cellular networks.
Mark Hallen, Bochong Li, Yu Tanouchi, Cheemeng Tan, Mike West

PLoS Comput Biol· October 2011

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Mass spectrometry- and lysine amidination-based protocol for thermodynamic analysis of protein folding and ligand binding interactions.
Ying Xu, Irene N Falk, Mark A Hallen, Michael C Fitzgerald

Anal Chem· May 2011

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Two-state displacement by the kinesin-14 Ncd stalk.
Mark A Hallen, Zhang-Yi Liang, Sharyn A Endow

Biophys Chem· March 2011

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Anastral spindle assembly and γ-tubulin in Drosophila oocytes.
Sharyn A Endow, Mark A Hallen

BMC Cell Biol· January 2011

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Expanding the scope of quantitative FRAP analysis.
Mark A Hallen, Anita T Layton

J Theor Biol· January 2010

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Anastral spindle assembly: a mathematical model.
Mark A Hallen, Sharyn A Endow

Biophys J· October 2009

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Mature Drosophila meiosis I spindles comprise microtubules of mixed polarity.
Zhang-Yi Liang, Mark Andrew Hallen, Sharyn Anne Endow

Curr Biol· January 2009

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Ncd motor binding and transport in the spindle.
Mark A Hallen, Zhang-Yi Liang, Sharyn A Endow

J Cell Sci· November 2008

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Fluorescence recovery kinetic analysis of gamma-tubulin binding to the mitotic spindle.
Mark A Hallen, Jianghai Ho, Christine D Yankel, Sharyn A Endow

Biophys J· September 2008

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A microtubule-destabilizing kinesin motor regulates spindle length and anchoring in oocytes.
Jianwei Zou, Mark A Hallen, Christine D Yankel, Sharyn A Endow

J Cell Biol· February 2008

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