User contributions for WikiSysop

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

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

06:4006:40, 20 August 2024 diff hist +1,645 N 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..." current
06:3906:39, 20 August 2024 diff hist +90 Main Page →3D Reconstruction
06:2506:25, 20 August 2024 diff hist +1,508 N 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..." current
06:2506:25, 20 August 2024 diff hist +98 Main Page →Image alignment
06:2006:20, 20 August 2024 diff hist +1,666 N 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..." current
06:1906:19, 20 August 2024 diff hist +68 Main Page →Fitting and docking
06:0706:07, 20 August 2024 diff hist +1,523 N 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..." current
06:0606:06, 20 August 2024 diff hist +102 Main Page →3D Reconstruction

06:2606:26, 19 August 2024 diff hist +1,516 N 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..." current
06:2506:25, 19 August 2024 diff hist +95 Main Page →Subtomogram analysis

06:1606:16, 16 August 2024 diff hist +1,311 N 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..." current
06:1506:15, 16 August 2024 diff hist +88 Main Page →Sample preparation
06:0606:06, 16 August 2024 diff hist +1,239 N 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..." current
06:0506:05, 16 August 2024 diff hist +80 Main Page →Books and reviews
05:5605:56, 16 August 2024 diff hist +1,697 N 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..." current
05:5405:54, 16 August 2024 diff hist +74 Main Page →Software
05:5105:51, 16 August 2024 diff hist +1,708 N 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..." current
05:5005:50, 16 August 2024 diff hist +105 Main Page →3D Heterogeneity

06:3106:31, 14 August 2024 diff hist +1,083 N 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..." current
06:3006:30, 14 August 2024 diff hist +89 Main Page →Books and reviews
06:2606:26, 14 August 2024 diff hist +1,388 N 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..." current
06:2506:25, 14 August 2024 diff hist +80 Main Page →Books and reviews
06:1906:19, 14 August 2024 diff hist +1,363 N 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..." current
06:1806:18, 14 August 2024 diff hist +72 Main Page →Books and reviews
05:5805:58, 14 August 2024 diff hist +2,019 N 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..." current
05:5805:58, 14 August 2024 diff hist +79 Main Page →Fitting and docking

User contributions for WikiSysop

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