User contributions for WikiSysop

09:3709:37, 8 November 2024 diff hist +1,482 N 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..." current
09:3409:34, 8 November 2024 diff hist +78 Main Page →2D Preprocessing

14:4814:48, 22 October 2024 diff hist +1,209 N 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..." current
14:4814:48, 22 October 2024 diff hist +67 Main Page →Books and reviews

06:5206:52, 18 October 2024 diff hist +2,232 N 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..." current
06:5106:51, 18 October 2024 diff hist +85 Main Page →Segmentation
06:4006:40, 18 October 2024 diff hist +1,459 N 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..." current
06:3906:39, 18 October 2024 diff hist +78 Main Page →Validation
05:5505:55, 18 October 2024 diff hist +1,644 N 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..." current
05:5405:54, 18 October 2024 diff hist +71 Main Page →3D reconstruction
05:3105:31, 18 October 2024 diff hist +1,784 N 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..." current
05:3105:31, 18 October 2024 diff hist 0 Main Page →3D Alignment
05:3005:30, 18 October 2024 diff hist +77 Main Page →3D Alignment

10:5410:54, 8 October 2024 diff hist +1,605 N 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..." current
10:5310:53, 8 October 2024 diff hist +89 Main Page →Subtomogram analysis

17:0317:03, 7 October 2024 diff hist +1,456 N 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..." current
17:0317:03, 7 October 2024 diff hist +91 Main Page →Sample preparation

06:5606:56, 6 September 2024 diff hist +1,904 N 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..." current
06:5506:55, 6 September 2024 diff hist +92 Main Page →3D Alignment
06:4906:49, 6 September 2024 diff hist +2,167 N 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..." current
06:4806:48, 6 September 2024 diff hist +82 Main Page →3D Alignment
06:3806:38, 6 September 2024 diff hist +1,960 N 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..." current
06:3706:37, 6 September 2024 diff hist +117 Main Page →Image alignment
06:3206:32, 6 September 2024 diff hist +1,535 N 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..." current
06:3106:31, 6 September 2024 diff hist +104 Main Page →Fitting and docking

06:4106:41, 5 September 2024 diff hist +1,439 N 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..." current
06:4006:40, 5 September 2024 diff hist +88 Main Page →3D Heterogeneity
06:3306:33, 5 September 2024 diff hist +1,740 N 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..." current
06:3206:32, 5 September 2024 diff hist +117 Main Page →Subtomogram analysis

07:2207:22, 4 September 2024 diff hist +221 Main Page →Electron microscopy images
06:4706:47, 4 September 2024 diff hist +1,179 N 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..." current
06:4606:46, 4 September 2024 diff hist +91 Main Page →Automatic particle picking
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

User contributions for WikiSysop

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