Measurement of atom resolvability in cryo-EM maps with Q-scores.


:Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. Q-scores can be calculated for atoms in proteins, nucleic acids, water, ligands and other solvent atoms, using models fitted to or derived from cryo-EM maps. Q-scores can also be averaged to represent larger features such as entire residues and nucleotides. Averaged over entire models, Q-scores correlate very well with the estimated resolution of cryo-EM maps for both protein and RNA. Assuming the models they are calculated from are well fitted to the map, Q-scores can be used as a measure of resolvability in cryo-EM maps at various scales, from entire macromolecules down to individual atoms. Q-score analysis of multiple cryo-EM maps of the same proteins derived from different laboratories confirms the reproducibility of structural features from side chains down to water and ion atoms.


Nat Methods


Nature methods


Pintilie G,Zhang K,Su Z,Li S,Schmid MF,Chiu W




Has Abstract


2020-03-01 00:00:00














  • An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.

    abstract::We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Corces MR,Trevino AE,Hamilton EG,Greenside PG,Sinnott-Armstrong NA,Vesuna S,Satpathy AT,Rubin AJ,Montine KS,Wu B,Kathiria A,Cho SW,Mumbach MR,Carter AC,Kasowski M,Orloff LA,Risca VI,Kundaje A,Khavari PA,Montine TJ,

    更新日期:2017-10-01 00:00:00

  • A probability-based approach for the analysis of large-scale RNAi screens.

    abstract::We describe a statistical analysis methodology designed to minimize the impact of off-target activities upon large-scale RNA interference (RNAi) screens in mammalian cells. Application of this approach enhances reconfirmation rates and facilitates the experimental validation of new gene activities through the probabil...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: König R,Chiang CY,Tu BP,Yan SF,DeJesus PD,Romero A,Bergauer T,Orth A,Krueger U,Zhou Y,Chanda SK

    更新日期:2007-10-01 00:00:00

  • A multiplexed homogeneous fluorescence-based assay for protein kinase activity in cell lysates.

    abstract::New methods to quantify protein kinase activities directly from complex cellular mixtures are critical for understanding biological regulatory pathways. Herein, a fluorescence-based chemosensor strategy for the direct measurement of kinase activities in crude mammalian cell lysates is described. We first designed a ne...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Shults MD,Janes KA,Lauffenburger DA,Imperiali B

    更新日期:2005-04-01 00:00:00

  • Tracking protein aggregation and mislocalization in cells with flow cytometry.

    abstract::We applied pulse-shape analysis (PulSA) to monitor protein localization changes in mammalian cells by flow cytometry. PulSA enabled high-throughput tracking of protein aggregation, translocation from the cytoplasm to the nucleus and trafficking from the plasma membrane to the Golgi as well as stress-granule formation....

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Ramdzan YM,Polling S,Chia CP,Ng IH,Ormsby AR,Croft NP,Purcell AW,Bogoyevitch MA,Ng DC,Gleeson PA,Hatters DM

    更新日期:2012-03-18 00:00:00

  • Author Correction: Resolution upgrades for light-sheet microscopy.

    abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    journal_title:Nature methods

    pub_type: 已发布勘误


    authors: Fiolka R

    更新日期:2019-10-01 00:00:00

  • In vivo three-photon imaging of activity of GCaMP6-labeled neurons deep in intact mouse brain.

    abstract::High-resolution optical imaging is critical to understanding brain function. We demonstrate that three-photon microscopy at 1,300-nm excitation enables functional imaging of GCaMP6s-labeled neurons beyond the depth limit of two-photon microscopy. We record spontaneous activity from up to 150 neurons in the hippocampal...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Ouzounov DG,Wang T,Wang M,Feng DD,Horton NG,Cruz-Hernández JC,Cheng YT,Reimer J,Tolias AS,Nishimura N,Xu C

    更新日期:2017-04-01 00:00:00

  • EPIC: software toolkit for elution profile-based inference of protein complexes.

    abstract::Protein complexes are key macromolecular machines of the cell, but their description remains incomplete. We and others previously reported an experimental strategy for global characterization of native protein assemblies based on chromatographic fractionation of biological extracts coupled to precision mass spectromet...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Hu LZ,Goebels F,Tan JH,Wolf E,Kuzmanov U,Wan C,Phanse S,Xu C,Schertzberg M,Fraser AG,Bader GD,Emili A

    更新日期:2019-08-01 00:00:00

  • Cell-type specific sequencing of microRNAs from complex animal tissues.

    abstract::MicroRNAs (miRNAs) play an essential role in the post-transcriptional regulation of animal development and physiology. However, in vivo studies aimed at linking miRNA function to the biology of distinct cell types within complex tissues remain challenging, partly because in vivo miRNA-profiling methods lack cellular r...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Alberti C,Manzenreither RA,Sowemimo I,Burkard TR,Wang J,Mahofsky K,Ameres SL,Cochella L

    更新日期:2018-04-01 00:00:00

  • A transgenic mouse for in vivo detection of endogenous labeled mRNA.

    abstract::Live-cell single mRNA imaging is a powerful tool but has been restricted in higher eukaryotes to artificial cell lines and reporter genes. We describe an approach that enables live-cell imaging of single endogenous labeled mRNA molecules transcribed in primary mammalian cells and tissue. We generated a knock-in mouse ...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Lionnet T,Czaplinski K,Darzacq X,Shav-Tal Y,Wells AL,Chao JA,Park HY,de Turris V,Lopez-Jones M,Singer RH

    更新日期:2011-02-01 00:00:00

  • Fluorescent indicators for simultaneous reporting of all four cell cycle phases.

    abstract::A robust method for simultaneous visualization of all four cell cycle phases in living cells is highly desirable. We developed an intensiometric reporter of the transition from S to G2 phase and engineered a far-red fluorescent protein, mMaroon1, to visualize chromatin condensation in mitosis. We combined these new re...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Bajar BT,Lam AJ,Badiee RK,Oh YH,Chu J,Zhou XX,Kim N,Kim BB,Chung M,Yablonovitch AL,Cruz BF,Kulalert K,Tao JJ,Meyer T,Su XD,Lin MZ

    更新日期:2016-12-01 00:00:00

  • Three-dimensional nanoscopy of whole cells and tissues with in situ point spread function retrieval.

    abstract::Single-molecule localization microscopy is a powerful tool for visualizing subcellular structures, interactions and protein functions in biological research. However, inhomogeneous refractive indices inside cells and tissues distort the fluorescent signal emitted from single-molecule probes, which rapidly degrades res...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Xu F,Ma D,MacPherson KP,Liu S,Bu Y,Wang Y,Tang Y,Bi C,Kwok T,Chubykin AA,Yin P,Calve S,Landreth GE,Huang F

    更新日期:2020-05-01 00:00:00

  • Molecular engineering: Unnatural design.

    abstract::Researchers designed an enzyme to carry out the Diels-Alder reaction, an activity not found in nature. ...

    journal_title:Nature methods

    pub_type: 评论,杂志文章


    authors: Doerr A

    更新日期:2010-09-01 00:00:00

  • Strategy for the fine characterization of glycosyltransferase specificity using isotopomer assembly.

    abstract::Glycosylation, which represents the most complex posttranslational modification (PTM) event during protein maturation, has a vital role in biological processes. Glycan biosynthesis is orchestrated by numerous glycosyltransferases, each displaying different selectivities for multiple reaction sites. The precise specifi...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Ito H,Kameyama A,Sato T,Sukegawa M,Ishida HK,Narimatsu H

    更新日期:2007-07-01 00:00:00

  • In vivo quantification of spatially varying mechanical properties in developing tissues.

    abstract::The mechanical properties of the cellular microenvironment and their spatiotemporal variations are thought to play a central role in sculpting embryonic tissues, maintaining organ architecture and controlling cell behavior, including cell differentiation. However, no direct in vivo and in situ measurement of mechanica...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Serwane F,Mongera A,Rowghanian P,Kealhofer DA,Lucio AA,Hockenbery ZM,Campàs O

    更新日期:2017-02-01 00:00:00

  • Chemically defined generation of human cardiomyocytes.

    abstract::Existing methods for human induced pluripotent stem cell (hiPSC) cardiac differentiation are efficient but require complex, undefined medium constituents that hinder further elucidation of the molecular mechanisms of cardiomyogenesis. Using hiPSCs derived under chemically defined conditions on synthetic matrices, we s...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Burridge PW,Matsa E,Shukla P,Lin ZC,Churko JM,Ebert AD,Lan F,Diecke S,Huber B,Mordwinkin NM,Plews JR,Abilez OJ,Cui B,Gold JD,Wu JC

    更新日期:2014-08-01 00:00:00

  • Single-cell systems biology by super-resolution imaging and combinatorial labeling.

    abstract::Fluorescence microscopy is a powerful quantitative tool for exploring regulatory networks in single cells. However, the number of molecular species that can be measured simultaneously is limited by the spectral overlap between fluorophores. Here we demonstrate a simple but general strategy to drastically increase the ...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Lubeck E,Cai L

    更新日期:2012-06-03 00:00:00

  • A photoprotection strategy for microsecond-resolution single-molecule fluorescence spectroscopy.

    abstract::Time resolution of current single-molecule fluorescence techniques is limited to milliseconds because of dye blinking and bleaching. Here we introduce a photoprotection strategy that affords microsecond resolution by combining efficient triplet quenching by oxygen and Trolox with minimized bleaching via the oxygen rad...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Campos LA,Liu J,Wang X,Ramanathan R,English DS,Muñoz V

    更新日期:2011-02-01 00:00:00

  • High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe.

    abstract::Epistasis analysis, which reports on the extent to which the function of one gene depends on the presence of a second, is a powerful tool for studying the functional organization of the cell. Systematic genome-wide studies of epistasis, however, have been limited, with the majority of data being collected in the buddi...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Roguev A,Wiren M,Weissman JS,Krogan NJ

    更新日期:2007-10-01 00:00:00

  • Bending the genome.

    abstract:: ...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Rusk N

    更新日期:2019-01-01 00:00:00

  • Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq.

    abstract::Massively parallel single-cell and single-nucleus RNA sequencing has opened the way to systematic tissue atlases in health and disease, but as the scale of data generation is growing, so is the need for computational pipelines for scaled analysis. Here we developed Cumulus-a cloud-based framework for analyzing large-s...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Li B,Gould J,Yang Y,Sarkizova S,Tabaka M,Ashenberg O,Rosen Y,Slyper M,Kowalczyk MS,Villani AC,Tickle T,Hacohen N,Rozenblatt-Rosen O,Regev A

    更新日期:2020-08-01 00:00:00

  • Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy.

    abstract::High-speed, large-scale three-dimensional (3D) imaging of neuronal activity poses a major challenge in neuroscience. Here we demonstrate simultaneous functional imaging of neuronal activity at single-neuron resolution in an entire Caenorhabditis elegans and in larval zebrafish brain. Our technique captures the dynamic...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Prevedel R,Yoon YG,Hoffmann M,Pak N,Wetzstein G,Kato S,Schrödel T,Raskar R,Zimmer M,Boyden ES,Vaziri A

    更新日期:2014-07-01 00:00:00

  • Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data.

    abstract::t-distributed stochastic neighbor embedding (t-SNE) is widely used for visualizing single-cell RNA-sequencing (scRNA-seq) data, but it scales poorly to large datasets. We dramatically accelerate t-SNE, obviating the need for data downsampling, and hence allowing visualization of rare cell populations. Furthermore, we ...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Linderman GC,Rachh M,Hoskins JG,Steinerberger S,Kluger Y

    更新日期:2019-03-01 00:00:00

  • Two-color, two-photon uncaging of glutamate and GABA.

    abstract::We developed a caged GABA (gamma-aminobutyric acid), which, when combined with an appropriate caged glutamate, allows bimodal control of neuronal membrane potential with subcellular resolution using optically independent two-photon uncaging of each neurotransmitter. We used two-color, two-photon uncaging to fire and b...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Kantevari S,Matsuzaki M,Kanemoto Y,Kasai H,Ellis-Davies GC

    更新日期:2010-02-01 00:00:00

  • Simultaneous mesoscopic and two-photon imaging of neuronal activity in cortical circuits.

    abstract::Spontaneous and sensory-evoked activity propagates across varying spatial scales in the mammalian cortex, but technical challenges have limited conceptual links between the function of local neuronal circuits and brain-wide network dynamics. We present a method for simultaneous cellular-resolution two-photon calcium i...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Barson D,Hamodi AS,Shen X,Lur G,Constable RT,Cardin JA,Crair MC,Higley MJ

    更新日期:2020-01-01 00:00:00

  • Quantifying domain-ligand affinities and specificities by high-throughput holdup assay.

    abstract::Many protein interactions are mediated by small linear motifs interacting specifically with defined families of globular domains. Quantifying the specificity of a motif requires measuring and comparing its binding affinities to all its putative target domains. To this end, we developed the high-throughput holdup assay...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Vincentelli R,Luck K,Poirson J,Polanowska J,Abdat J,Blémont M,Turchetto J,Iv F,Ricquier K,Straub ML,Forster A,Cassonnet P,Borg JP,Jacob Y,Masson M,Nominé Y,Reboul J,Wolff N,Charbonnier S,Travé G

    更新日期:2015-08-01 00:00:00

  • Enhanced antibody validation.

    abstract:: ...

    journal_title:Nature methods

    pub_type: 评论,杂志文章


    authors: Doerr A

    更新日期:2018-12-01 00:00:00

  • Three-dimensional biomaterials for the study of human pluripotent stem cells.

    abstract::The self-renewal and differentiation of human pluripotent stem cells (hPSCs) have typically been studied in flat, two-dimensional (2D) environments. In this Perspective, we argue that 3D model systems may be needed in addition, as they mimic the natural 3D tissue organization more closely. We survey methods that have ...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Kraehenbuehl TP,Langer R,Ferreira LS

    更新日期:2011-08-30 00:00:00

  • Imaging cellular network dynamics in three dimensions using fast 3D laser scanning.

    abstract::Spatiotemporal activity patterns in three-dimensionally organized cellular networks are fundamental to the function of the nervous system. Despite advances in functional imaging of cell populations, a method to resolve local network activity in three dimensions has been lacking. Here we introduce a three-dimensional (...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Göbel W,Kampa BM,Helmchen F

    更新日期:2007-01-01 00:00:00

  • The inside tag.

    abstract::An uncharged CoA precursor that can enter the cell is used for covalent, site-specific labeling of proteins inside living cells. ...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Kaganman I

    更新日期:2006-11-01 00:00:00

  • Atmospheric pressure MALDI mass spectrometry imaging of tissues and cells at 1.4-μm lateral resolution.

    abstract::We report an atmospheric pressure (AP) matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) setup with a lateral resolution of 1.4 μm, a mass resolution greater than 100,000, and accuracy below ±2 p.p.m. We achieved this by coupling a focusing objective with a numerical aperture (NA) of ...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Kompauer M,Heiles S,Spengler B

    更新日期:2017-01-01 00:00:00