All public logs

Combined display of all available logs of 3DEM-Methods. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).

• 15:07, 18 November 2024 WikiSysop talk contribs created page 2024deLaRosa EMHub (Created page with "== Citation == J. M. de la Rosa-Trevin et al., “EMhub: a web platform for data management and on-the-fly processing in scientific facilities,” Biological Crystallography, vol. 80, no. 11, 2024. == Abstract == Most scientific facilities produce large amounts of heterogeneous data at a rapid pace. Managing users, instruments, reports and invoices presents additional challenges. To address these challenges, EMhub, a web platform designed to support the daily operatio...")
• 10:31, 8 November 2024 WikiSysop talk contribs created page 2024Cameron REPIC (Created page with "== Citation == C. J. Cameron, S. J. Seager, F. J. Sigworth, H. D. Tagare, and M. B. Gerstein, “REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers,” Communications Biology, vol. 7, no. 1, p. 1421, 2024. == Abstract == Cryo-EM particle identification from micrographs (“picking”) is challenging due to the low signal-to-noise ratio and lack of ground truth for particle locations. State-of-the-art computa...")
• 10:28, 8 November 2024 WikiSysop talk contribs created page 2024Li EM2NA (Created page with "== Citation == T. Li, H. Cao, J. He, and S.-Y. Huang, “Automated detection and de novo structure modeling of nucleic acids from cryo-EM maps,” Nature Communications, vol. 15, no. 1, p. 9367, 2024. == Abstract == Cryo-electron microscopy (cryo-EM) is one of the most powerful experimental methods for macromolecular structure determination. However, accurate DNA/RNA structure modeling from cryo-EM maps is still challenging especially for protein-DNA/RNA or multi-chai...")
• 10:22, 8 November 2024 WikiSysop talk contribs created page 2024Ermel DataPortal (Created page with "== Citation == U. Ermel et al., “A data portal for providing standardized annotations for cryo-electron tomography,” Nature Methods, pp. 1–3, 2024. == Abstract == We present the cryoET Data Portal (https://cryoetdataportal. czscience.com/), containing annotated cryoET datasets in standardized formats, as a resource for the cryoET community == Keywords == == Links == https://www.nature.com/articles/s41592-024-02477-2 == Related software == == Related methods...")
• 10:16, 8 November 2024 WikiSysop talk contribs created page 2024Wang DiffModeller (Created page with "== Citation == X. Wang, H. Zhu, G. Terashi, M. Taluja, and D. Kihara, “DiffModeler: large macromolecular structure modeling for cryo-EM maps using a diffusion model,” Nature Methods, pp. 1–11, 2024. == Abstract == Cryogenic electron microscopy (cryo-EM) has now been widely used for determining multichain protein complexes. However, modeling a large complex structure, such as those with more than ten chains, is challenging, particularly when the map resolution de...")
• 10:11, 8 November 2024 WikiSysop talk contribs created page 2024Anuk Auction (Created page with "== Citation == S. Anuk, T. Bendory, and A. Painsky, “Image detection using combinatorial auction,” IEEE Open J. Signal Processing, 2024. == Abstract == This paper studies the optimal solution of the classical problem of detecting the location of multiple image occurrences in a two-dimensional, noisy measurement. Assuming the image occurrences do not overlap, we formulate this task as a constrained maximum likelihood optimization problem.We show that the maximum li...")
• 10:06, 8 November 2024 WikiSysop talk contribs created page 2024Chen EModelX (Created page with "== Citation == S. Chen, S. Zhang, X. Fang, L. Lin, H. Zhao, and Y. Yang, “Protein complex structure modeling by cross-modal alignment between cryo-EM maps and protein sequences,” Nature Communications, vol. 15, no. 1, p. 8808, 2024. == Abstract == Cryo-electron microscopy (cryo-EM) technique is widely used for protein structure determination. Current automatic cryo-EM protein complex modeling methods mostly rely on prior chain separation. However, chain separation...")
• 10:00, 8 November 2024 WikiSysop talk contribs created page 2024Moriya GoToCloud (Created page with "== Citation == T. Moriya, Y. Yamada, M. Yamamoto, and T. Senda, “GoToCloud optimization of cloud computing environment for accelerating cryo-EM structure-based drug design,” Communications Biology, vol. 7, no. 1, p. 1320, 2024. == Abstract == Cryogenic electron microscopy (Cryo-EM) is a widely used technique for visualizing the 3D structures of many drug design targets, including membrane proteins, at atomic resolution. However, the necessary throughput for struct...")
• 09:46, 8 November 2024 WikiSysop talk contribs created page 2024Joosten Roodmus (Created page with "== Citation == M. Joosten, J. Greer, J. Parkhurst, T. Burnley, and A. J. Jakobi, “Roodmus: A toolkit for benchmarking heterogeneous electron cryo-microscopy reconstructions,” IUCrJ, vol. 11, no. 6, 2024. == Abstract == Conformational heterogeneity of biological macromolecules is a challenge in single-particle averaging (SPA). Current standard practice is to employ classification and filtering methods that may allow a discrete number of conformational states to be...")
• 09:37, 8 November 2024 WikiSysop talk contribs created page 2024Li Subtraction (Created page with "== Citation == S. Li, M. Li, Y. Wang, and X. Li, “Subtraction of liposome signals in cryo-EM structural determination of protein-liposome complexes,” Chinese Physics B, 2024. == Abstract == Reconstituting membrane proteins in liposomes and determining their structure is a common method for determining membrane protein structures using single-particle cryo-electron microscopy (cryo-EM). However, the strong signal of liposomes under cryo-EM imaging conditions often...")
• 14:48, 22 October 2024 WikiSysop talk contribs created page 2024Lander Validation (Created page with "== Citation == G. C. Lander, “Single particle cryo-EM map and model validation: It’s not crystal clear,” Current Opinion in Structural Biology, vol. 89, p. 102918, 2024. == Abstract == The application of single particle cryogenic electron microscopy (cryo-EM) to structure determination continues to have a transformative impact on our understanding on biological systems. While there has been a great deal of algorithmic development focused on improving attainable...")
• 06:52, 18 October 2024 WikiSysop talk contribs created page 2023Sazzed Struwwel (Created page with "== Citation == S. Sazzed, P. Scheible, J. He, and W. Wriggers, “Untangling irregular actin cytoskeleton architectures in tomograms of the cell with struwwel tracer,” Intl. J. Molecular Sciences, vol. 24, no. 24, p. 17183, 2023. == Abstract == In this work, we established, validated, and optimized a novel computational framework for tracing arbitrarily oriented actin filaments in cryo-electron tomography maps. Our approach was designed for highly complex intracellu...")
• 06:40, 18 October 2024 WikiSysop talk contribs created page 2024Sanchez Anisotropy (Created page with "== Citation == R. Sanchez-Garcia, G. Gaullier, J. M. Cuadra-Troncoso, and J. Vargas, “Cryo-EM map anisotropy can be attenuated by map post-processing and a new method for its estimation,” Intl. J. Molecular Sciences, vol. 25, no. 7, p. 3959, 2024. == Abstract == One of the most important challenges in cryogenic electron microscopy (cryo-EM) is the substantial number of samples that exhibit preferred orientations, which leads to an uneven coverage of the projection...")
• 05:55, 18 October 2024 WikiSysop talk contribs created page 2024vanVeen Missing (Created page with "== Citation == D. Van Veen et al., “Missing wedge completion via unsupervised learning with coordinate networks,” Intl. J. Molecular Sciences, vol. 25, no. 10, p. 5473, 2024. == Abstract == Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction qua...")
• 05:31, 18 October 2024 WikiSysop talk contribs created page 2023Ling Synch (Created page with "== Citation == S. Ling, “Solving orthogonal group synchronization via convex and low-rank optimization: Tightness and landscape analysis,” Mathematical Programming, vol. 200, no. 1, pp. 589–628, 2023. == Abstract == Group synchronization aims to recover the group elements from their noisy pairwise measurements. It has found many applications in community detection, clock synchronization, and joint alignment problem. This paper focuses on the orthogonal group syn...")
• 10:54, 8 October 2024 WikiSysop talk contribs created page 2024Huang MiLoPYP (Created page with "== Citation == Q. Huang, Y. Zhou, and A. Bartesaghi, “MiLoPYP: self-supervised molecular pattern mining and particle localization in situ,” Nature Methods, pp. 1–10, 2024. == Abstract == Cryo-electron tomography allows the routine visualization of cellular landscapes in three dimensions at nanometer-range resolutions. When combined with single-particle tomography, it is possible to obtain near-atomic resolution structures of frequently occurring macromolecules w...")
• 17:03, 7 October 2024 WikiSysop talk contribs created page 2024Abe LEA (Created page with "== Citation == K. M. Abe, G. Li, Q. He, T. Grant, and C. J. Lim, “Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing,” Nature Communications, vol. 15, no. 1, p. 7705, 2024. == Abstract == Air-water interface (AWI) interactions during cryo-electron microscopy (cryo-EM) sample preparation cause significant sample loss, hindering structural biology research. Organisms like nematodes and tardigrades produce Late Em...")
• 06:56, 6 September 2024 WikiSysop talk contribs created page 2022Levy CryoAI (Created page with "== Citation == Levy, Axel / Poitevin, Frédéric / Martel, Julien / Nashed, Youssef / Peck, Ariana / Miolane, Nina / Ratner, Daniel / Dunne, Mike / Wetzstein, Gordon. Cryoai: Amortized inference of poses for ab initio reconstruction of 3d molecular volumes from real cryo-em images. 2022. European Conference on Computer Vision, p. 540-557 == Abstract == Cryo-electron microscopy (cryo-EM) has become a tool of fundamental importance in structural biology, helping us unde...")
• 06:49, 6 September 2024 WikiSysop talk contribs created page 2023Rangan Fast (Created page with "== Citation == Rangan, Aaditya V. Radial recombination for rigid rotational alignment of images and volumes. 2023. Inverse Problems, Vol. 39, No. 1, p. 015003 == Abstract == A common task in single particle electron cryomicroscopy (cryo-EM) is the rigid alignment of images and/or volumes. In the context of images, a rigid alignment involves estimating the inner product between one image of N × N pixels and another image that has been translated by some displaceme...")
• 06:38, 6 September 2024 WikiSysop talk contribs created page 2022Ganguly SparseAlign (Created page with "== Citation == Ganguly, Poulami Somanya / Lucka, Felix / Kohr, Holger / Franken, Erik / Hupkes, Hermen Jan / Batenburg, Kees Joost. Sparsealign: A grid-free algorithm for automatic marker localization and deformation estimation in cryo-electron tomography. 2022. IEEE Transactions on Computational Imaging, Vol. 8, p. 651-665 == Abstract == Tilt-series alignment is crucial to obtaining high-resolution reconstructions in cryo-electron tomography. Beam-induced local defor...")
• 06:32, 6 September 2024 WikiSysop talk contribs created page 2022Terwilliger AlphaFold (Created page with "== Citation == Terwilliger, Thomas C. / Poon, Billy K. / Afonine, Pavel V. / Schlicksup, Christopher J. / Croll, Tristan I. / Millán, Claudia / Richardson, Jane S. / Read, Randy J. / Adams, Paul D. Improved AlphaFold modeling with implicit experimental information. 2022. Nature methods, Vol. 19, No. 11, p. 1376-1382 == Abstract == Machine-learning prediction algorithms such as AlphaFold and RoseTTAFold can create remarkably accurate protein models, but these models u...")
• 06:41, 5 September 2024 WikiSysop talk contribs created page 2022Arnold liganded (Created page with "== Citation == Arnold, William R. / Asarnow, Daniel / Cheng, Yifan. Classifying liganded states in heterogeneous single-particle cryo-EM datasets. 2022. Microscopy, Vol. 71, No. Supplement_1, p. i23-i29 == Abstract == A powerful aspect of single-particle cryogenic electron microscopy is its ability to determine high-resolution structures from samples containing heterogeneous mixtures of the same macromolecule in different conformational or compositional states. Beyond...")
• 06:33, 5 September 2024 WikiSysop talk contribs created page 2021Moebel DeepFinder (Created page with "== Citation == Moebel, Emmanuel / Martinez-Sanchez, Antonio / Lamm, Lorenz / Righetto, Ricardo D. / Wietrzynski, Wojciech / Albert, Sahradha / Larivière, Damien / Fourmentin, Eric / Pfeffer, Stefan / Ortiz, Julio / others. Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms. 2021. Nature methods, Vol. 18, No. 11, p. 1386-1394 Abstract: Cryogenic electron tomography (cryo-ET) visualizes the 3D spatial distribution of macromolecule...")
• 06:47, 4 September 2024 WikiSysop talk contribs created page 2022Kreymer MTD (Created page with "== Citation == Kreymer, Shay / Singer, Amit / Bendory, Tamir. An approximate expectation-maximization for two-dimensional multi-target detection. 2022. IEEE signal processing letters, Vol. 29, p. 1087-1091 == Abstract == We consider the two-dimensional multi-target detection (MTD) problem of estimating a target image from a noisy measurement that contains multiple copies of the image, each randomly rotated and translated. The MTD model serves as a mathematical abstrac...")
• 06:41, 4 September 2024 WikiSysop talk contribs created page 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...")
• 06:26, 4 September 2024 WikiSysop talk contribs created page 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...")
• 06:11, 4 September 2024 WikiSysop talk contribs created page 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...")
• 05:26, 4 September 2024 WikiSysop talk contribs created page 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...")
• 05:18, 4 September 2024 WikiSysop talk contribs created page 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...")
• 05:13, 4 September 2024 WikiSysop talk contribs created page 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...")
• 05:09, 4 September 2024 WikiSysop talk contribs created page 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...")
• 05:02, 4 September 2024 WikiSysop talk contribs created page 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)....")
• 04:51, 4 September 2024 WikiSysop talk contribs created page 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...")
• 12:46, 3 September 2024 WikiSysop talk contribs created page 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...")
• 12:44, 3 September 2024 WikiSysop talk contribs created page 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...")
• 12:32, 3 September 2024 WikiSysop talk contribs created page 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...")
• 07:04, 3 September 2024 WikiSysop talk contribs created page 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...")
• 06:17, 3 September 2024 WikiSysop talk contribs created page 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...")
• 06:08, 3 September 2024 WikiSysop talk contribs created page 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...")
• 06:02, 3 September 2024 WikiSysop talk contribs created page 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...")
• 08:39, 26 August 2024 User account Amartinez talk contribs was created by WikiSysop talk contribs and password was sent by email (Cuenta para Antonio)
• 11:56, 21 August 2024 WikiSysop talk contribs created page 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...")
• 11:45, 21 August 2024 WikiSysop talk contribs created page 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...")
• 11:31, 21 August 2024 WikiSysop talk contribs created page 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...")
• 07:05, 21 August 2024 WikiSysop talk contribs created page 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...")
• 06:53, 21 August 2024 WikiSysop talk contribs created page 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...")
• 06:25, 21 August 2024 WikiSysop talk contribs created page 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...")
• 06:14, 21 August 2024 WikiSysop talk contribs created page 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...")
• 06:09, 21 August 2024 WikiSysop talk contribs created page 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....")
• 05:54, 21 August 2024 WikiSysop talk contribs created page 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...")