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Articles by Scott Classen
PARP1-HPF1 structure and dynamics on nicked DNA suggest a mechanism for acute and localized ADP-ribosylation - Nature Communications
Abstract PARP1 detection of DNA strand breaks allosterically leads to PARP1 synthesis of poly(ADP-ribose) modifications that signal DNA damage. HPF1 engages activated PARP1 to control modification site selection. Understanding of the mechanism of DNA break detection and catalytic activation is incomplete, due largely to limited structural information for full-length PARP1.
Predicting RNA structure and dynamics with deep learning and solution scattering
Significance Understanding the behavior of RNA in solution is critical for deciphering its biological functions, yet predicting its macromolecular conformation remains challenging. While advanced computational methods can predict RNA structures, their accuracy in solution is often limited by the absence of stabilizing ions and the failure to account for RNA’s conformational flexibility.
Predicting RNA Structure and Dynamics with Deep Learning and Solution Scattering
Abstract While novel deep learning and statistics-based techniques predict accurate structural models for proteins and non-coding RNA, describing their macromolecular conformations in solution is still challenging. Small-angle X-ray scattering (SAXS) in solution is an efficient technique to validate structural predictions by comparing the experimental SAXS profile with those calculated from predicted structures.
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Strong epistasis constrains the evolution of strict substrate specificity in apicomplexan lactate dehydrogenases
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