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Crystal structure, conformational fixation, and entry-related interactions of mature ligand-free HIV-1 Env
TLDR
Antigenicity-guided structural design can be used both to delineate mechanism and to fix conformation, with DS-Env trimers in virus-like-particle and soluble formats providing a new generation of vaccine antigens. Expand
Dead‐end elimination with perturbations (DEEPer): A provable protein design algorithm with continuous sidechain and backbone flexibility
TLDR
A new algorithm, DEEPer (Dead‐End Elimination with Perturbations), that combines the new abilities to handle arbitrarily large backbone perturbations and to generate ensembles of backbone conformations, providing significant advantages for modeling protein mutations and protein–ligand interactions. Expand
Compact Representation of Continuous Energy Surfaces for More Efficient Protein Design.
TLDR
It is demonstrated that EPIC efficiently represents the energy surface for both molecular-mechanics and quantum- mechanical energy functions, and is applied specifically to protein design for modeling both side chain and backbone degrees of freedom. Expand
A microtubule-destabilizing kinesin motor regulates spindle length and anchoring in oocytes
TLDR
It is reported that KLP10A localizes to the unusual pole bodies of anastral Drosophila melanogaster oocyte meiosis I spindles as well as spindle fibers, centromeres, and cortical microtubules, and may promote spindle reorientation upon oocyte activation by altering microtubule dynamics. Expand
Anastral spindle assembly and γ-tubulin in Drosophila oocytes
TLDR
The FRAP results, together with its mutant effects late in meiosis I, indicate that γTub37C may perform a role subsequent to metaphase I, rather than nucleating microtubules for meiosis II spindle formation. Expand
Fluorescence recovery kinetic analysis of gamma-tubulin binding to the mitotic spindle.
TLDR
Fluorescence recovery after photobleaching is used to analyze gamma-tubulin binding to the mitotic spindle and centrosomes to determine the role of gamma- Tubulin in microtubule nucleation in the spindle, implying that gamma- tubulin functions by binding weakly to spindle microtubules. Expand
OSPREY 3.0: Open‐source protein redesign for you, with powerful new features
TLDR
It is shown here empirically that osprey 3.0 accurately predicts the effect of mutations on protein–protein binding, and offers a unique package of advantages over other design software, including provable design algorithms that account for continuous flexibility during design and model conformational entropy. Expand
Expanding the scope of quantitative FRAP analysis.
TLDR
Numerical results show that using a model that represents the influential physical processes and that is formulated in the appropriate geometry can substantially improve the accuracy of FRAP calculations. Expand
CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions
TLDR
This work presents an efficient algorithm, CATS, for computing atomic coordinates as a function of the new continuous backbone internal coordinates, and shows that CATS can model the viability of an antibody mutation known experimentally to increase affinity, but that appears sterically infeasible when modeled with less or no backbone flexibility. Expand
Comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence
TLDR
Comets provides a new level of versatile, efficient, and provable multistate design that provably returns the minimum with respect to sequence of any desired linear combination of the energies of multiple protein states, subject to constraints on other linear combinations. Expand
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