User contributions for WikiSysop

Results for WikiSysop talk block log uploads logs
A user with 2,451 edits. Account created on 30 March 2009.
Jump to navigation Jump to search
Search for contributionsExpandCollapse
⧼contribs-top⧽
⧼contribs-date⧽
(newest | oldest) View ( | ) (20 | 50 | 100 | 250 | 500)

18 October 2024

8 October 2024

  • 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

7 October 2024

  • 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

6 September 2024

  • 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

5 September 2024

  • 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

4 September 2024

  • 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

3 September 2024

  • 12:4612:46, 3 September 2024 diff hist +1,061 N 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..." current
  • 12:4512:45, 3 September 2024 diff hist +75 Main Page →Books and reviews
  • 12:4412:44, 3 September 2024 diff hist +2,541 N 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..." current
  • 12:3912:39, 3 September 2024 diff hist +69 Main Page →Segmentation
  • 12:3212:32, 3 September 2024 diff hist +1,160 N 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..." current
  • 12:3112:31, 3 September 2024 diff hist +69 Main Page →3D Reconstruction
  • 07:0407:04, 3 September 2024 diff hist +1,847 N 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..." current
  • 07:0307:03, 3 September 2024 diff hist +93 Main Page →Fitting and docking
  • 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
(newest | oldest) View ( | ) (20 | 50 | 100 | 250 | 500)
Retrieved from "https://3demmethods.i2pc.es/index.php/Special:Contributions/WikiSysop"