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- 05:02, 4 September 2024 2021Singer Wilson (hist | edit) [1,354 bytes] WikiSysop (talk | contribs) (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)....")
- 04:51, 4 September 2024 2021Danev Eval (hist | edit) [2,023 bytes] WikiSysop (talk | contribs) (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...")
- 12:46, 3 September 2024 2020Wigge Review (hist | edit) [1,061 bytes] WikiSysop (talk | contribs) (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...")
- 12:44, 3 September 2024 2022Ranno Neural (hist | edit) [2,541 bytes] WikiSysop (talk | contribs) (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...")
- 12:32, 3 September 2024 2022Lan RCT (hist | edit) [1,160 bytes] WikiSysop (talk | contribs) (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...")
- 07:04, 3 September 2024 2022Bouvier coevolution (hist | edit) [1,847 bytes] WikiSysop (talk | contribs) (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...")
- 06:17, 3 September 2024 2024Fan CryoTrans (hist | edit) [1,630 bytes] WikiSysop (talk | contribs) (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...")
- 06:08, 3 September 2024 2024Gucwa CMM (hist | edit) [1,798 bytes] WikiSysop (talk | contribs) (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...")
- 06:02, 3 September 2024 2024Agarwal crefDenoiser (hist | edit) [1,746 bytes] WikiSysop (talk | contribs) (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...")
- 11:56, 21 August 2024 2024Burt Relion5 (hist | edit) [1,457 bytes] WikiSysop (talk | contribs) (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...")
- 11:45, 21 August 2024 2024Hoff EMMIVox (hist | edit) [1,665 bytes] WikiSysop (talk | contribs) (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...")
- 11:31, 21 August 2024 2024Eisenstein SPACETomo (hist | edit) [1,206 bytes] WikiSysop (talk | contribs) (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...")
- 07:05, 21 August 2024 2024Esfahani SPOTRASTR (hist | edit) [2,189 bytes] WikiSysop (talk | contribs) (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...")
- 06:53, 21 August 2024 2024Schwab DynaMight (hist | edit) [1,397 bytes] WikiSysop (talk | contribs) (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...")
- 06:25, 21 August 2024 2024Xu MarkerAuto2 (hist | edit) [1,629 bytes] WikiSysop (talk | contribs) (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...")
- 06:14, 21 August 2024 2024Zhang CTFMeasure (hist | edit) [1,395 bytes] WikiSysop (talk | contribs) (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...")
- 06:09, 21 August 2024 2024Wlodarski cryoEnsemble (hist | edit) [1,634 bytes] WikiSysop (talk | contribs) (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....")
- 05:54, 21 August 2024 2024Klindt Disentanglement (hist | edit) [2,630 bytes] WikiSysop (talk | contribs) (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...")
- 06:40, 20 August 2024 2024Aiyer Workflow (hist | edit) [1,645 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Aiyer, Sriram / Baldwin, Philip R. / Tan, Shi Min / Shan, Zelin / Oh, Juntaek / Mehrani, Atousa / Bowman, Marianne E. / Louie, Gordon / Passos, Dario Oliveira / Đorđević-Marquardt, Selena / others. Overcoming resolution attenuation during tilted cryo-EM data collection. 2024. Nature communications, Vol. 15, No. 1, p. 389 == Abstract == Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting “prefe...")
- 06:25, 20 August 2024 2024Coray Automated (hist | edit) [1,508 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Coray, Raffaele / Navarro, Paula / Scaramuzza, Stefano / Stahlberg, Henning / Castaño-Diez, Daniel, Automated fiducial-based alignment of cryo-electron tomography tilt series in Dynamo, 2024, Structure, Vol. 32, p. 1-12 == Abstract == With the advent of modern technologies for cryo-electron tomography (cryo-ET), high-quality tilt series are more rapidly acquired than processed and analyzed. Thus, a robust and fast-automated alignment for batch processi...")
- 06:20, 20 August 2024 2024Read Interactive (hist | edit) [1,666 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Read, Randy J. / Pettersen, Eric F. / McCoy, Airlie J. / Croll, Tristan I. / Terwilliger, Thomas C. / Poon, Billy K. / Meng, Elaine C. / Liebschner, Dorothee / Adams, Paul D. Likelihood-based interactive local docking into cryo-EM maps in ChimeraX. 2024. Acta Crystallographica Section D, Vol. 80, p. 588-598 == Abstract == The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particular...")
- 06:07, 20 August 2024 2024Zhu SIRM (hist | edit) [1,523 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Zhu, Dongjie / Cao, Weili / Li, Junxi / Wu, Chunling / Cao, Duanfang / Zhang, Xinzheng. Correction of preferred orientation--induced distortion in cryo-electron microscopy maps. 2024. Science Advances, Vol. 10, No. 30, p. eadn0092 == Abstract == Reconstruction maps of cryo–electron microscopy (cryo-EM) exhibit distortion when the cryo-EM dataset is incomplete, usually caused by unevenly distributed orientations. Prior efforts had been attempted to ad...")
- 06:26, 19 August 2024 2024Rangan CryoDRGNET (hist | edit) [1,516 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Rangan, Ramya / Feathers, Ryan / Khavnekar, Sagar / Lerer, Adam / Johnston, Jake D. / Kelley, Ron / Obr, Martin / Kotecha, Abhay / Zhong, Ellen D. CryoDRGN-ET: deep reconstructing generative networks for visualizing dynamic biomolecules inside cells. 2024. Nature Methods, p. 1-9 == Abstract == Advances in cryo-electron tomography (cryo-ET) have produced new opportunities to visualize the structures of dynamic macromolecules in native cellular environmen...")
- 06:16, 16 August 2024 2024Liu Graphene (hist | edit) [1,311 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Liu, Nan / Wang, Hong-Wei. Graphene in cryo-EM specimen optimization. 2024. Current Opinion in Structural Biology, Vol. 86, p. 102823 == Abstract == Specimen preparation is a critical but challenging step in highresolution cryogenic electron microscopy (cryo-EM) structural analysis of macromolecules. In the past decade, graphene has gained much recognition as the supporting substrate to optimize cryo-EM specimen preparation. It improves macromolecule em...")
- 06:06, 16 August 2024 2024Hutchings Review (hist | edit) [1,239 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Hutchings, Joshua / Villa, Elizabeth. Expanding insights from in situ cryo-EM. 2024. Current Opinion in Structural Biology, Vol. 88, p. 102885 == Abstract == The combination of cryo-electron tomography and subtomogram analysis affords 3D high-resolution views of biological macromolecules in their native cellular environment, or in situ. Streamlined methods for acquiring and processing these data are advancing attainable resolutions into the realm of dru...")
- 05:56, 16 August 2024 2024Maurer PyTME (hist | edit) [1,697 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Maurer, Valentin J. / Siggel, Marc / Kosinski, Jan. PyTME (Python Template Matching Engine): A fast, flexible, and multi-purpose template matching library for cryogenic electron microscopy data. 2024. SoftwareX, Vol. 25, p. 101636 == Abstract == Cryogenic electron microscopy (cryo-EM) is a key method in structural and cell biology. Analysis of cryo-EM images requires interpretation of noisy, low-resolution densities, which relies on identifying the most...")
- 05:51, 16 August 2024 2024Song RMSFNet (hist | edit) [1,708 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Song, Xintao / Bao, Lei / Feng, Chenjie / Huang, Qiang / Zhang, Fa / Gao, Xin / Han, Renmin. Accurate Prediction of Protein Structural Flexibility by Deep Learning Integrating Intricate Atomic Structures and Cryo-EM Density Information. 2024. Nature Communications, Vol. 15, No. 1, p. 5538 == Abstract == The dynamics of proteins are crucial for understanding their mechanisms. However, computationally predicting protein dynamic information has proven chal...")