Search Results - "Hallen, Mark A."

Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env by Do Kwon, Young, Pancera, Marie, Acharya, Priyamvada, Georgiev, Ivelin S, Crooks, Emma T, Gorman, Jason, Joyce, M Gordon, Guttman, Miklos, Ma, Xiaochu, Narpala, Sandeep, Soto, Cinque, Terry, Daniel S, Yang, Yongping, Zhou, Tongqing, Ahlsen, Goran, Bailer, Robert T, Chambers, Michael, Chuang, Gwo-Yu, Doria-Rose, Nicole A, Druz, Aliaksandr, Hallen, Mark A, Harned, Adam, Kirys, Tatsiana, Louder, Mark K, O'Dell, Sijy, Ofek, Gilad, Osawa, Keiko, Prabhakaran, Madhu, Sastry, Mallika, Stewart-Jones, Guillaume B E, Stuckey, Jonathan, Thomas, Paul V, Tittley, Tishina, Williams, Constance, Zhang, Baoshan, Zhao, Hong, Zhou, Zhou, Donald, Bruce R, Lee, Lawrence K, Zolla-Pazner, Susan, Baxa, Ulrich, Schön, Arne, Freire, Ernesto, Shapiro, Lawrence, Lee, Kelly K, Arthos, James, Munro, James B, Blanchard, Scott C, Mothes, Walther, Binley, James M, McDermott, Adrian B, Mascola, John R, Kwong, Peter D

“…The structure of the ligand-free HIV-1–Env trimer allows conformational fixation of Env and generation of an antigen that binds CD4 with high affinity and is…”
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PLUG (Pruning of Local Unrealistic Geometries) removes restrictions on biophysical modeling for protein design by Hallen, Mark A.

“…Protein design algorithms must search an enormous conformational space to identify favorable conformations. As a result, those that perform this search with…”
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Altered nucleotide-microtubule coupling and increased mechanical output by a kinesin mutant by Liu, Hong-Lei, Hallen, Mark A, Endow, Sharyn A

“…Kinesin motors hydrolyze ATP to produce force and do work in the cell--how the motors do this is not fully understood, but is thought to depend on the coupling…”
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Ncd motor binding and transport in the spindle by Hallen, Mark A, Liang, Zhang-Yi, Endow, Sharyn A

“…The Ncd kinesin-14 motor is required for meiotic spindle assembly in Drosophila oocytes and produces force in mitotic spindles that opposes other motors…”
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microtubule-destabilizing kinesin motor regulates spindle length and anchoring in oocytes by Zou, Jianwei, Hallen, Mark A, Yankel, Christine D, Endow, Sharyn A

“…The kinesin-13 motor, KLP10A, destabilizes microtubules at their minus ends in mitosis and binds to polymerizing plus ends in interphase, regulating spindle…”
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Dead-end elimination with perturbations (DEEPer): A provable protein design algorithm with continuous sidechain and backbone flexibility by Hallen, Mark A., Keedy, Daniel A., Donald, Bruce R.

“…Computational protein and drug design generally require accurate modeling of protein conformations. This modeling typically starts with an experimentally…”
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CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions by Hallen, Mark A, Donald, Bruce R

“…When proteins mutate or bind to ligands, their backbones often move significantly, especially in loop regions. Computational protein design algorithms must…”
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OSPREY 3.0: Open‐source protein redesign for you, with powerful new features by Hallen, Mark A., Martin, Jeffrey W., Ojewole, Adegoke, Jou, Jonathan D., Lowegard, Anna U., Frenkel, Marcel S., Gainza, Pablo, Nisonoff, Hunter M., Mukund, Aditya, Wang, Siyu, Holt, Graham T., Zhou, David, Dowd, Elizabeth, Donald, Bruce R.

“…We present osprey 3.0, a new and greatly improved release of the osprey protein design software. Osprey 3.0 features a convenient new Python interface, which…”
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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 by Hallen, Mark A, Donald, Bruce R

“…Practical protein design problems require designing sequences with a combination of affinity, stability, and specificity requirements. Multistate protein…”
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Compact Representation of Continuous Energy Surfaces for More Efficient Protein Design by Hallen, Mark A, Gainza, Pablo, Donald, Bruce R

“…In macromolecular design, conformational energies are sensitive to small changes in atom coordinates; thus, modeling the small, continuous motions of atoms…”
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Fast gap-free enumeration of conformations and sequences for protein design by Roberts, Kyle E., Gainza, Pablo, Hallen, Mark A., Donald, Bruce R.

“…ABSTRACT Despite significant successes in structure‐based computational protein design in recent years, protein design algorithms must be improved to increase…”
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LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency by Hallen, Mark A, Jou, Jonathan D, Donald, Bruce R

“…Most protein design algorithms search over discrete conformations and an energy function that is residue-pairwise, that is, a sum of terms that depend on the…”
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Mass Spectrometry- and Lysine Amidination-Based Protocol for Thermodynamic Analysis of Protein Folding and Ligand Binding Interactions by Xu, Ying, Falk, Irene N, Hallen, Mark A, Fitzgerald, Michael C

“…Described here is a mass spectrometry-based covalent labeling protocol that utilizes the amine reactive reagent, s-methyl thioacetimidate (SMTA), to study the…”
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Fluorescence Recovery Kinetic Analysis of γ-Tubulin Binding to the Mitotic Spindle by Hallen, Mark A., Ho, Jianghai, Yankel, Christine D., Endow, Sharyn A.

“…Fluorescence recovery after photobleaching has been widely used to study dynamic processes in the cell, but less frequently to analyze binding interactions and…”
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Anastral Spindle Assembly: A Mathematical Model by Hallen, Mark A., Endow, Sharyn A.

“…Assembly of an anastral spindle was modeled as a two-stage process: first, the aggregation of microtubule foci or asters around the chromosomes, and second,…”
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Expanding the scope of quantitative FRAP analysis by Hallen, Mark A., Layton, Anita T.

“…In this study, new mathematical models were developed for analysis of fluorescence recovery after photobleaching (FRAP) data to account for features not…”
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Two-state displacement by the kinesin-14 Ncd stalk by Hallen, Mark A., Liang, Zhang-Yi, Endow, Sharyn A.

“…The nonprocessive kinesin-14 Ncd motor binds to microtubules and hydrolyzes ATP, undergoing a single displacement before releasing the microtubule. A…”
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Synthesis of Carboxylic Acid Monolayers by Ozonolysis of 10-Undecenyltrichlorosilane SAMs by Hallen, Mark A, Hallen, Hans D

“…A high-yield method has been developed for the production of carboxyl-terminated alkylsiloxane monolayers on silicon using the ozonolysis and hydrolysis of…”
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Anastral spindle assembly and γ-tubulin in Drosophila oocytes by Endow, Sharyn A, Hallen, Mark A

“…Anastral spindles assemble by a mechanism that involves microtubule nucleation and growth from chromatin. It is still uncertain whether γ-tubulin, a…”
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LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid-Rotamer-Like Efficiency by Hallen, Mark A., Jou, Jonathan D., Donald, Bruce R.

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