About: Non-uniform refinement: Adaptive regularization improves single particle cryo-EM reconstruction

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About: Non-uniform refinement: Adaptive regularization improves single particle cryo-EM reconstruction Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Non-uniform refinement: Adaptive regularization improves single particle cryo-EM reconstruction
Creator	Fleet, David Punjani, Ali Zhang, Haowei
Source	BioRxiv; MedRxiv
abstract	Single particle cryo-EM is a powerful method for studying proteins and other biological macromolecules. Many of these molecules comprise regions with varying structural properties including disorder, flexibility, and partial occupancy. These traits make computational 3D reconstruction from 2D images challenging. Detergent micelles and lipid nanodiscs, used to keep membrane proteins in solution, are common examples of locally disordered structures that can negatively affect existing iterative refinement algorithms which assume rigidity (or spatial uniformity). We introduce a cross-validation approach to derive non-uniform refinement, an algorithm that automatically regularizes 3D density maps during iterative refinement to account for spatial variability, yielding dramatically improved resolution and 3D map quality. We find that in common iterative refinement methods, regularization using spatially uniform filtering operations can simultaneously over- and under-regularize local regions of a 3D map. In contrast, non-uniform refinement removes noise in disordered regions while retaining signal useful for aligning particle images. Our results include state-of-the-art resolution 3D reconstructions of multiple membrane proteins with molecular weight as low as 90kDa. These results demonstrate that higher resolutions and improved 3D density map quality can be achieved even for small membrane proteins, an important use case for single particle cryo-EM, both in structural biology and drug discovery. Non-uniform refinement is implemented in the cryoSPARC software package and has already been used successfully in several notable structural studies.
has issue date	2019-12-16(xsd:dateTime)
bibo:doi	10.1101/2019.12.15.877092
has license	medrxiv
sha1sum (hex)	ffcfdf9b1ba722f4bfff8c71c65c93b0b64981a0
schema:url	https://doi.org/10.1101/2019.12.15.877092
resource representing a document's title	Non-uniform refinement: Adaptive regularization improves single particle cryo-EM reconstruction
schema:publication	bioRxiv
resource representing a document's body	covid:ffcfdf9b1ba722f4bfff8c71c65c93b0b64981a0#body_text
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