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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).

• 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...")
• 06:40, 20 August 2024 WikiSysop talk contribs created page 2024Aiyer Workflow (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 WikiSysop talk contribs created page 2024Coray Automated (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 WikiSysop talk contribs created page 2024Read Interactive (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 WikiSysop talk contribs created page 2024Zhu SIRM (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 WikiSysop talk contribs created page 2024Rangan CryoDRGNET (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 WikiSysop talk contribs created page 2024Liu Graphene (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 WikiSysop talk contribs created page 2024Hutchings Review (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 WikiSysop talk contribs created page 2024Maurer PyTME (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 WikiSysop talk contribs created page 2024Song RMSFNet (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...")
• 06:31, 14 August 2024 WikiSysop talk contribs created page 2024Bock MD (Created page with "== Citation == Bock, Lars V. / Igaev, Maxim / Grubmüller, Helmut. Single-particle Cryo-EM and molecular dynamics simulations: A perfect match. 2024. Current Opinion in Structural Biology, Vol. 86, p. 102825 == Abstract == Knowledge of the structure and dynamics of biomolecules is key to understanding the mechanisms underlying their biological functions. Single-particle cryo-electron microscopy (cryo-EM) is a powerful structural biology technique to characterize compl...")
• 06:26, 14 August 2024 WikiSysop talk contribs created page 2024Kimanius Heterogeneity (Created page with "== Citation == Kimanius, Dari / Schwab, Johannes. Confronting heterogeneity in cryogenic electron microscopy data: Innovative strategies and future perspectives with data-driven methods. 2024. Current Opinion in Structural Biology, Vol. 86, p. 102815 == Abstract == The surge in the influx of data from cryogenic electron microscopy (cryo-EM) experiments has intensified the demand for robust algorithms capable of autonomously managing structurally heterogeneous dataset...")
• 06:19, 14 August 2024 WikiSysop talk contribs created page 2024Cheng Automated (Created page with "== Citation == Cheng, Anchi / Yu, Yue. Recent advances in data collection for Cryo-EM methods. 2024. Current Opinion in Structural Biology, Vol. 86, p. 102795 == Abstract == Methods of transmission electron microscopy (TEM) are typically used to resolve structures of vitrified biological specimens using both single particle analysis (SPA) and tomographic methods and use both conventional as well as scanning transmission modes of data collection. Automation of data col...")
• 05:58, 14 August 2024 WikiSysop talk contribs created page 2024Wankowicz qFit (Created page with "== Citation == Wankowicz, Stephanie A. / Ravikumar, Ashraya / Sharma, Shivani / Riley, Blake / Raju, Akshay / Hogan, Daniel W. / Flowers, Jessica / van den Bedem, Henry / Keedy, Daniel A. / Fraser, James S. Automated multiconformer model building for X-ray crystallography and cryo-EM. 2024. eLife, Vol. 12, p. RP90606 == Abstract == In their folded state, biomolecules exchange between multiple conformational states that are crucial for their function. Traditional struc...")
• 05:47, 14 August 2024 WikiSysop talk contribs created page 2024Giri CryoStruct (Created page with "== Citation == Giri, Nabin / Cheng, Jianlin. De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM. 2024. Nature Communications, Vol. 15, No. 1, p. 5511 == Abstract == Accurately building 3D atomic structures from cryo-EM density maps is a crucial step in cryo-EM-based protein structure determination. Converting density maps into 3D atomic structures for proteins lacking accurate homologous or predicted structures as templates...")
• 06:50, 13 August 2024 WikiSysop talk contribs created page 2024Lytje SAXS (Created page with "== Citation == Lytje, Kristian / Pedersen, Jan Skov. Validation of electron-microscopy maps using solution small-angle X-ray scattering. 2024. Acta Crystallographica Section D: Structural Biology, Vol. 80, No. 7, p. 493-505 == Abstract == The determination of the atomic resolution structure of biomacromolecules is essential for understanding details of their function. Traditionally, such a structure determination has been performed with crystallographic or nuclear res...")
• 06:35, 13 August 2024 WikiSysop talk contribs created page 2024Xu Miffi (Created page with "== Citation == Xu, Da / Ando, Nozomi. Miffi: Improving the accuracy of CNN-based cryo-EM micrograph filtering with fine-tuning and Fourier space information. 2024. J. Structural Biology, Vol. 216, No. 2, p. 108072 == Abstract == Efficient and high-accuracy filtering of cryo-electron microscopy (cryo-EM) micrographs is an emerging challenge with the growing speed of data collection and sizes of datasets. Convolutional neural networks (CNNs) are machine learning models...")
• 06:28, 13 August 2024 WikiSysop talk contribs created page 2024Siggel ColabSeg (Created page with "== Citation == Siggel, Marc / Jensen, Rasmus K. / Maurer, Valentin J. / Mahamid, Julia / Kosinski, Jan. ColabSeg: An interactive tool for editing, processing, and visualizing membrane segmentations from cryo-ET data. 2024. J. Structural Biology, Vol. 216, No. 2, p. 108067 == Abstract == Cellular cryo-electron tomography (cryo-ET) has emerged as a key method to unravel the spatial and structural complexity of cells in their near-native state at unprecedented molecular...")
• 06:23, 13 August 2024 WikiSysop talk contribs created page 2024Jin Size (Created page with "== Citation == Jin, Weisheng / Zhou, Ye / Bartesaghi, Alberto. Accurate size-based protein localization from cryo-ET tomograms. 2024. J. Structural Biology X, Vol. 10, p. 100104 == Abstract == Cryo-electron tomography (cryo-ET) combined with sub-tomogram averaging (STA) allows the determination of protein structures imaged within the native context of the cell at near-atomic resolution. Particle picking is an essential step in the cryo-ET/STA image analysis pipeline t...")
• 07:14, 12 August 2024 WikiSysop talk contribs created page 2024Cruz Template (Created page with "== Citation == Cruz-León, Sergio / Majtner, Tomáš / Hoffmann, Patrick / Kreysing, Jan P. / Tuijtel, Maarten W. / Schaefer, Stefan L. / Geißler, Katharina / Beck, Martin / Turoňová, Beata / Hummer, Gerhard. High-confidence 3D template matching for cryo-electron tomography. 2024. Biophysical Journal, Vol. 123, No. 3, p. 183a == Abstract == Visual proteomics attempts to build atlases of the molecular content of cells but the automated annotation of cryo electron to...")
• 07:03, 12 August 2024 WikiSysop talk contribs created page 2024Bowlby Flexible (Created page with "== Citation == Bowlby, Beatrice. The dynamic duo: cryo-EM teams up with machine learning to visualize biomolecules in motion. 2024. Biotechniques, Vol. 76, p. 229-233 == Abstract == Cryo-EM has been a key technique in our understanding of biomolecular structures. Now, machine learning techniques are being used to put these structures in motion, revealing dynamic interactions and processes happening on a molecular and cellular level. == Keywords == == Links == https...")
• 06:56, 12 August 2024 WikiSysop talk contribs created page 2024Sazzed CryoSSESeg (Created page with "== Citation == Sazzed, Salim. Determining Protein Secondary Structures in Heterogeneous Medium-Resolution Cryo-EM Images Using CryoSSESeg. 2024. ACS Omega == Abstract == While the acquisition of cryo-electron microscopy (cryo-EM) at near-atomic resolution is becoming more prevalent, a considerable number of density maps are still resolved only at intermediate resolutions (5−10 Å). Due to the large variation in quality among these medium-resolution density maps, ext...")
• 06:24, 12 August 2024 WikiSysop talk contribs created page 2024Dahmani MDFF (Created page with "== Citation == Dahmani, Zakaria L. / Scott, Ana Ligia / Vénien-Bryan, Catherine / Perahia, David / Costa, Mauricio G. S. MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search. 2024. J. Chemical Information and Modeling, Vol. 64, No. 13, p. 5151-5160 == Abstract == Molecular Dynamics Flexible Fitting (MDFF) is a widely used tool to refine high-resolution structures into cryo-EM density maps. Despit...")
• 06:16, 12 August 2024 WikiSysop talk contribs created page 2023Watson Review (Created page with "== Citation == Watson, Abigail J. I. / Bartesaghi, Alberto. Advances in cryo-ET data processing: meeting the demands of visual proteomics. 2024. Current Opinion in Structural Biology, Vol. 87 p. 102861 == Abstract == Cryogenic electron tomography (cryo-ET), a method that enables the viewing of biomolecules in near-native environments at high resolution, is rising in accessibility and applicability. Over the past several years, once slow sample preparation and data col...")