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4 September 2024
- 06:4106:41, 4 September 2024 diff hist +1,849 N 2022Bendory Complexity Created page with "== Citation == Bendory, Tamir / Mickelin, Oscar / Singer, Amit. Sparse multi-reference alignment: Sample complexity and computational hardness. 2022. ICASSP 2022-2022 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), p. 8977-8981 == Abstract == Motivated by the problem of determining the atomic structure of macromolecules using single-particle cryo-electron microscopy (cryo-EM), we study the sample and computational complexities of th..." current
- 06:4006:40, 4 September 2024 diff hist +108 Main Page →2D Alignment
- 06:2606:26, 4 September 2024 diff hist +2,423 N 2022Bandyopadhyay Adaptation Created page with "== Citation == Bandyopadhyay, Hmrishav / Deng, Zihao / Ding, Leiting / Liu, Sinuo / Uddin, Mostofa Rafid / Zeng, Xiangrui / Behpour, Sima / Xu, Min. Cryo-shift: reducing domain shift in cryo-electron subtomograms with unsupervised domain adaptation and randomization. 2022. Bioinformatics, Vol. 38, No. 4, p. 977-984 == Abstract == Motivation Cryo-Electron Tomography (cryo-ET) is a 3D imaging technology that enables the visualization of subcellular structures in situ at..." current
- 06:2506:25, 4 September 2024 diff hist +136 Main Page →Subtomogram analysis
- 06:1106:11, 4 September 2024 diff hist +1,341 N 2022Warshamanage EMDA Created page with "== Citation == Warshamanage, Rangana / Yamashita, Keitaro / Murshudov, Garib N. EMDA: A Python package for Electron Microscopy Data Analysis. 2022. Journal of structural biology, Vol. 214, p. 107826 == Abstract == An open-source Python library EMDA for cryo-EM map and model manipulation is presented with a specific focus on validation. The use of several functionalities in the library is presented through several examples. The utility of local correlation as a metric..." current
- 06:1006:10, 4 September 2024 diff hist +113 Main Page →Software
- 05:2605:26, 4 September 2024 diff hist +1,517 N 2022Seitz ESPER Created page with "== Citation == Seitz, Evan / Acosta-Reyes, Francisco / Maji, Suvrajit / Schwander, Peter / Frank, Joachim. Recovery of conformational continuum from single-particle Cryo-EM images: Optimization of ManifoldEM informed by ground truth. 2022. IEEE transactions on computational imaging, Vol. 8, p. 462-478 == Abstract == This work is based on the manifold-embedding approach to study biological molecules exhibiting continuous conformational changes. Previous work establishe..." current
- 05:2505:25, 4 September 2024 diff hist +71 Main Page →3D Heterogeneity
- 05:1805:18, 4 September 2024 diff hist +1,599 N 2022Lian Neural Created page with "== Citation == Lian, Ruyi / Huang, Bingyao / Wang, Liguo / Liu, Qun / Lin, Yuewei / Ling, Haibin. End-to-end orientation estimation from 2D cryo-EM images. 2022. Acta Crystallographica Section D: Structural Biology, Vol. 78, No. 2, p. 174-186 == Abstract == Cryo-electron microscopy (cryo-EM) is a Nobel Prize-winning technique for determining high-resolution 3D structures of biological macromolecules. A 3D structure is reconstructed from hundreds of thousands of noisy..." current
- 05:1805:18, 4 September 2024 diff hist +79 Main Page →3D Alignment
- 05:1305:13, 4 September 2024 diff hist +1,506 N 2021Nair PDBe Created page with "== Citation == Nair, Sreenath / Varadi, Mihaly / Nadzirin, Nurul / Pravda, Lukáš / Anyango, Stephen / Mir, Saqib / Berrisford, John / Armstrong, David / Gutmanas, Aleksandras / Velankar, Sameer. PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data. 2021. Bioinformatics, Vol. 37, No. 21, p. 3950-3952 == Abstract == Summary The PDBe aggregated API is an open-access and open-source RESTful API that provides programmatic..." current
- 05:1205:12, 4 September 2024 diff hist +44 Main Page →Databases
- 05:0905:09, 4 September 2024 diff hist +1,513 N 2022Pant ExitWave Created page with "== Citation == Pant, Apoorv / Banerjee, Manidipa / Khare, Kedar. Quantitative phase imaging of single particles from a cryoEM micrograph. 2022. Optics Communications, Vol. 506, p. 127588 == Abstract == We show that de-focused single particle micrographs recorded using a cryo-electron microscope (cryoEM) system may be processed like a Fresnel zone in-line hologram to obtain physically meaningful quantitative phase maps associated with individual particles. In particula..." current
- 05:0805:08, 4 September 2024 diff hist +76 Main Page →CTF estimation and restoration
- 05:0205:02, 4 September 2024 diff hist +1,354 N 2021Singer Wilson Created page with "== Citation == Singer, Amit. Wilson statistics: derivation, generalization and applications to electron cryomicroscopy. 2021. Acta Crystallographica Section A: Foundations and Advances, Vol. 77, No. 5, p. 472-479 == Abstract == The power spectrum of proteins at high frequencies is remarkably well described by the flat Wilson statistics. Wilson statistics therefore plays a significant role in X-ray crystallography and more recently in electron cryomicroscopy (cryo-EM)...." current
- 05:0105:01, 4 September 2024 diff hist +78 Main Page →Image formation
- 04:5104:51, 4 September 2024 diff hist +2,023 N 2021Danev Eval Created page with "== Citation == Danev, Radostin / Yanagisawa, Haruaki / Kikkawa, Masahide. Cryo-EM performance testing of hardware and data acquisition strategies. 2021. Microscopy, Vol. 70, No. 6, p. 487-497 == Abstract == The increasing popularity and adoption rate of cryo-electron microscopy (cryo-EM) is evidenced by a growing number of new microscope installations around the world. The quality and reliability of the instruments improved dramatically in recent years, but site-speci..." current
- 04:5004:50, 4 September 2024 diff hist +90 Main Page →Automated data collection
3 September 2024
- 12:4612:46, 3 September 2024 diff hist +1,061 N 2020Wigge Review Created page with "== Citation == Wigge, Christoph / Stefanovic, Aleksandar / Radjainia, Mazdak. The rapidly evolving role of cryo-EM in drug design. 2020. Drug Discovery Today: Technologies, Vol. 38, p. 91-102 == Abstract == Since the early 2010s, cryo-electron microscopy (cryoEM) has evolved to a mainstream structural biology method in what has been dubbed the ``resolution revolution”. Pharma companies also began to use cryo-EM in drug discovery, evidenced by a growing number of ind..." current
- 12:4512:45, 3 September 2024 diff hist +75 Main Page →Books and reviews
- 12:4412:44, 3 September 2024 diff hist +2,541 N 2022Ranno Neural Created page with "== Citation == Ranno, Nathan / Si, Dong. Neural representations of cryo-EM maps and a graph-based interpretation. 2022. BMC bioinformatics, Vol. 23, No. Suppl 3, p. 397 == Abstract == Background: Advances in imagery at atomic and near-atomic resolution, such as cryogenic electron microscopy (cryo-EM), have led to an influx of high resolution images of proteins and other macromolecular structures to data banks worldwide. Producing a protein structure from the discrete..." current
- 12:3912:39, 3 September 2024 diff hist +69 Main Page →Segmentation
- 12:3212:32, 3 September 2024 diff hist +1,160 N 2022Lan RCT Created page with "== Citation == Lan, T.-Y. / Boumal, Nicolas / Singer, Amit. Random conical tilt reconstruction without particle picking in cryo-electron microscopy. 2022. Acta Crystallographica Section A: Foundations and Advances, Vol. 78, No. 4, p. 294-301 == Abstract == A method is proposed to reconstruct the 3D molecular structure from micrographs collected at just one sample tilt angle in the random conical tilt scheme in cryo-electron microscopy. The method uses autocorrelation..." current
- 12:3112:31, 3 September 2024 diff hist +69 Main Page →3D Reconstruction
- 07:0407:04, 3 September 2024 diff hist +1,847 N 2022Bouvier coevolution Created page with "== Citation == Bouvier, Guillaume / Bardiaux, Benjamin / Pellarin, Riccardo / Rapisarda, Chiara / Nilges, Michael. Building Protein Atomic Models from Cryo-EM Density Maps and Residue Co-evolution. 2022. Biomolecules, Vol. 12, No. 9, p. 1290 == Abstract == Electron cryo-microscopy (cryo-EM) has emerged as a powerful method by which to obtain three-dimensional (3D) structures of macromolecular complexes at atomic or near-atomic resolution. However, de novo building of..." current
- 07:0307:03, 3 September 2024 diff hist +93 Main Page →Fitting and docking
- 06:1706:17, 3 September 2024 diff hist +1,630 N 2024Fan CryoTrans Created page with "== Citation == Fan, Xiao / Zhang, Qi / Zhang, Hui / Zhu, Jianying / Ju, Lili / Shi, Zuoqiang / Hu, Mingxu / Bao, Chenglong. CryoTRANS: predicting high-resolution maps of rare conformations from self-supervised trajectories in cryo-EM. 2024. Communications Biology, Vol. 7, No. 1, p. 1058 == Abstract == Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a comm..." current
- 06:1706:17, 3 September 2024 diff hist +91 Main Page →3D Heterogeneity
- 06:0806:08, 3 September 2024 diff hist +1,798 N 2024Gucwa CMM Created page with "== Citation == Gucwa, Michal / Bijak, Vanessa / Zheng, Heping / Murzyn, Krzysztof / Minor, Wladek. CheckMyMetal (CMM): validating metal-binding sites in X-ray and cryo-EM data. 2024. IUCrJ, Vol. 11, No. 5 == Abstract == Identifying and characterizing metal-binding sites (MBS) within macromolecular structures is imperative for elucidating their biological functions. CheckMyMetal (CMM) is a web based tool that facilitates the interactive validation of MBS in structure..." current
- 06:0606:06, 3 September 2024 diff hist +80 Main Page →Fitting and docking
- 06:0206:02, 3 September 2024 diff hist +1,746 N 2024Agarwal crefDenoiser Created page with "== Citation == Agarwal, Ishaant / Kaczmar-Michalska, Joanna / Noerrelykke, Simon F. / Rzepiela, Andrzej. Refinement of Cryo-EM 3D Maps with Self-Supervised Denoising Model: crefDenoiser. 2024. IUCR J, Vol. 11, p. 821-830 == Abstract == Cryogenic electron microscopy (cryo-EM) is a pivotal technique for imaging macromolecular structures. However, despite extensive processing of large image sets collected in cryo-EM experiments to amplify the signal-to-noise ratio, the..." current
- 05:5905:59, 3 September 2024 diff hist +97 Main Page →Sharpening of high resolution information
21 August 2024
- 11:5611:56, 21 August 2024 diff hist +1,457 N 2024Burt Relion5 Created page with "== Citation == Burt, Alister / Toader, Bogdan / Warshamanage, Rangana / von Kügelgen, Andriko / Pyle, Euan / Zivanov, Jasenko / Kimanius, Dari / Bharat, Tanmay A. M. / Scheres, Sjors H. W. An image processing pipeline for electron cryo-tomography in RELION-5. 2024. FEBS Open Bio == Abstract == Electron tomography of frozen, hydrated samples allows structure determination of macromolecular complexes that are embedded in complex environments. Provided that the target c..." current
- 11:5511:55, 21 August 2024 diff hist +73 Main Page →Software
- 11:4511:45, 21 August 2024 diff hist +1,665 N 2024Hoff EMMIVox Created page with "== Citation == Hoff, Samuel E. / Thomasen, F. Emil / Lindorff-Larsen, Kresten / Bonomi, Massimiliano. Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference. 2024. PLOS Computational Biology, Vol. 20, No. 7, p. e1012180 == Abstract == Converting cryo-electron microscopy (cryo-EM) data into high-quality structural models is a challenging problem of outstanding importance. Current refinement methods often generate unbalanced mo..." current
- 11:4411:44, 21 August 2024 diff hist +100 Main Page →Fitting and docking
- 11:3111:31, 21 August 2024 diff hist +1,206 N 2024Eisenstein SPACETomo Created page with "== Citation == Eisenstein, Fabian / Fukuda, Yoshiyuki / Danev, Radostin. Smart parallel automated cryo-electron tomography. 2024. Nature Methods, p. 1-4 == Abstract == In situ cryo-electron tomography enables investigation of macromolecules in their native cellular environment. Samples have become more readily available owing to recent software and hardware advancements. Data collection, however, still requires an experienced operator and appreciable microscope time t..." current
- 11:3011:30, 21 August 2024 diff hist +83 Main Page →Automated data collection
- 07:0507:05, 21 August 2024 diff hist +2,189 N 2024Esfahani SPOTRASTR Created page with "== Citation == Esfahani, Behrouz Ghazi / Randolph, Peter S. / Peng, Ruizhi / Stroupe, Elizabeth / Grant, Tim / Stagg, Scott M. SPOT-RASTR—a cryo-EM specimen preparation technique that overcomes problems with preferred orientation and the air/water interface. 2024. PNAS Nexus, Vol. 3, p. 184 == Abstract == In cryogenic electron microscopy (cryo-EM), specimen preparation remains a bottleneck despite recent advancements. Classical plunge freezing methods often result i..." current
- 07:0507:05, 21 August 2024 diff hist +124 Main Page →Sample preparation
- 06:5306:53, 21 August 2024 diff hist +1,397 N 2024Schwab DynaMight Created page with "== Citation == Schwab, Johannes / Kimanius, Dari / Burt, Alister / Dendooven, Tom / Scheres, Sjors H. W. DynaMight: estimating molecular motions with improved reconstruction from cryo-EM images. 2024. Nature Methods, p. 1-8 == Abstract == How to deal with continuously flexing molecules is one of the biggest outstanding challenges in single-particle analysis of proteins from cryogenic-electron microscopy (cryo-EM) images. Here, we present DynaMight, a software tool tha..." current
- 06:5206:52, 21 August 2024 diff hist +98 Main Page →3D Heterogeneity
- 06:2506:25, 21 August 2024 diff hist +1,629 N 2024Xu MarkerAuto2 Created page with "== Citation == Xu, Zihe / Li, Hongjia / Wan, Xiaohua / Fernández, Jose-Jesus / Sun, Fei / Zhang, Fa / Han, Renmin. Markerauto2: A fast and robust fully automatic fiducial marker-based tilt series alignment software for electron tomography. 2024. Structure, Vol. 32, p. 1-12 == Abstract == Cryoelectron tomography (cryo-ET) has become an indispensable technology for visualizing in situ biological ultrastructures, where the tilt series alignment is the key step to obtain..." current
- 06:2406:24, 21 August 2024 diff hist +91 Main Page →Image alignment
- 06:1406:14, 21 August 2024 diff hist +1,395 N 2024Zhang CTFMeasure Created page with "== Citation == Zhang, Ranhao / Shen, Yuan / Li, Xueming. Tilt-series-based joint CTF estimation for cryo-electron tomography. 2024. Structure, Vol. 32, p. 1239-1247 == Abstract == Contrast transfer function (CTF) estimation is a necessary step in the cryo-electron tomography (cryoET) workflow and essential for high-resolution in situ structural determination. However, the low signal-to-noise ratio and continuous defocus variation in micrographs of cryoET tilt series m..." current
- 06:1106:11, 21 August 2024 diff hist +94 Main Page →CTF estimation and restoration
- 06:0906:09, 21 August 2024 diff hist +1,634 N 2024Wlodarski cryoEnsemble Created page with "== Citation == Włodarski, Tomasz / Streit, Julian O. / Mitropoulou, Alkistis / Cabrita, Lisa D. / Vendruscolo, Michele / Christodoulou, John. Bayesian reweighting of biomolecular structural ensembles using heterogeneous cryo-EM maps with the cryoENsemble method. 2024. Scientific Reports, Vol. 14, No. 1, p. 18149 == Abstract == Cryogenic electron microscopy (cryo-EM) has emerged as a powerful method for the determination of structures of complex biological molecules...." current
- 06:0806:08, 21 August 2024 diff hist +132 Main Page →Fitting and docking
- 05:5405:54, 21 August 2024 diff hist +2,630 N 2024Klindt Disentanglement Created page with "== Citation == Klindt, David A. / Hyvärinen, Aapo / Levy, Axel / Miolane, Nina / Poitevin, Frédéric. Towards interpretable Cryo-EM: disentangling latent spaces of molecular conformations. 2024. Frontiers in Molecular Biosciences, Vol. 11, p. 1393564 == Abstract == Molecules are essential building blocks of life and their different conformations (i.e., shapes) crucially determine the functional role that they play in living organisms. Cryogenic Electron Microscopy..." current
- 05:5305:53, 21 August 2024 diff hist +146 Main Page →3D Heterogeneity