[3dem] Now Online: Frontiers in Cryo-EM Modeling
Willy Wriggers
wriggers at biomachina.org
Mon Jun 15 13:34:50 PDT 2020
Dear 3DEM community,
Our previously announced "Special Issue on Frontiers in Cryo-EM
Modeling" has just been been published in the Journal of Chemical
Information and Modeling at https://urldefense.com/v3/__https://pubs.acs.org/toc/jcisd8/60/5__;!!Mih3wA!UY38MwKzCLGc7gLHkVpzbdTbjFQ0mn5tCtl--c74igAh4PCEg-Zry1QaHJRICgcBdg$ .
The 26 contributions provide a timely benchmark in our research field.
Below, please find a brief overview of relevant topics and senior
authors (abridged from the editorial).
Thank you for your interest and happy reading!
Willy Wriggers (also on behalf of co-editors Giulia Palermo, Yuji
Sugita, and Rommie E. Amaro).
---
Relating to a recent discussion on this list, Nobel laureate Joachim
Frank contributed two papers on what has been informally called "cryoEM
Dynamics" (see 3DEM forum messages on May 25 and 26, 2020). Several
other perspectives on the value of contemporary cryoEM modeling include
the potential impact of cryoEM in structure prediction approaches by
Abriata and Dal Peraro, assessing the impact of computational modeling
at the atomic level by Fraser, Lindorff-Larsen, and Bonomi, and how
cryoEM stands to impact cellular-scale structural-omics type studies by
McCafferty and colleagues. A review by Sengupta and coauthors covers
advances in sample preparation and molecular modeling, whereas one by
Ivanov and colleagues discusses recent advances and applications of
flexible-fitting approaches for data refinement. Cossio discusses the
need for and challenges related to cross-validation for developed
models. Sanbonmatsu and colleagues, as well as Kellogg and Cianfrocco,
present thoughtful contributions on potential cryoEM-modeling workflow
pitfalls and best practices.
Methodological advances in integrative modeling cover a wide range of
aspects and related experimental approaches. Wriggers and colleagues
present a template-based deconvolution and denoising approach that
corrects for missing wedge artifacts in tomograms of cytoskeletal
filaments. Tama and co-workers present an in-depth look at pixel-size
parameters for improving cryoEM maps. Winn and Joseph and colleagues
demonstrate a novel method for calculating differences between a cryoEM
map and a fitted model that uses amplitude matching in resolution
shells, as well as show its utility in highlighting conformational and
compositional differences. Cole and colleagues develop
ImageDataExtractor, which identifies and extracts microscopy images from
the scientific literature, presenting them for use in data-driven
materials discovery-type approaches. Kihara and co-workers develop new
software, MAINMASTseg, to improve map segmentation and results for
cryoEM data sets with multiple chains. He and colleagues establish a
cylindrical F1 score similarity metric for alpha-helices in cryoEM maps
that provides a classifier for database validation studies as well as a
criterion to assess the local quality of maps and their associated
atomic models.
Several groups present new tools to improve the end-to-end cryoEM
working procedures. Shen and co-workers present a fully automated
toolkit, SPREAD, for 3D reconstruction that uses a network-based image
clustering algorithm. Marabini and colleagues present a major update to
their framework Scipion that improves model building and provenance of
the complete workflow. Schenk and co-workers present CryoFLARE, an
open-source platform for integrating various processing algorithms and
development of automated workflows.
Molecular dynamics flexible fitting remains a popular approach for
fitting atomic resolution models into density maps, as also reviewed by
Ivanov and colleagues. A number of groups present extensions and
improvements to the method. Lindert and Leelananda demonstrate how
integrating NMR chemical shifts into cryoEM density restraints improves
refinement results. Singharoy and co-workers present a new method that
integrates neural network potentials together with quantum
mechanical/molecular mechanics methods to improve on fitting small
molecules into cryoEM maps. A related method presented by Costa and
colleagues, MDeNM-EMfit, extends molecular dynamics with excited normal
modes in a way that directs sampling toward conformations that have high
correlations with the density maps.
Finally, several groups contributed applications to interesting
biological systems. Magistrato and colleagues show how MD together with
cryoEM provides never before seen insight into splicing modulators.
Ravelli and co-workers show how processing algorithm improvements
improved size limits for cryoEM using hen egg white lysozyme. Llorca and
colleagues present their strategy for modeling the medium-density
RUVBL2-binding domain, as well as subsequent simulations to explore
biological hypotheses about its interactions with RNA polymerase II.
Worrall and co-workers provide a historical perspective of cryoEM
studies of the type III secretion system needle complex as well as
describe their own workflow that enabled the successful determination of
the whole complex.
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