New pages

05:5705:57, 3 September 2026 2026Sun QwenCryoMarker (hist | edit) [3,256 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Sun, Y., Zhao, J., Xu, N., Wang, L., Ding, W. and Li, M. 2026. QwenCryoMarker: a universal post-processing framework for contamination-aware particle cleaning. Acta Crystallographica Sec. D. 82, 9 (2026). == Abstract == Cryo-electron microscopy (cryo-EM) micrographs are frequently contaminated by carbon edges, ice crystals, ethane bubbles and other high-contrast artifacts. These contaminants trigger abundant false positives in automated particle pickers...")

04:3704:37, 31 August 2026 2026Kreymer EM (hist | edit) [1,456 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Kreymer, S., Singer, A. and Bendory, T. 2026. Expectation-maximization for structure determination directly from cryo-em micrographs. Inverse problems and imaging. 27, (2026), 110. == Abstract == A single-particle cryo-electron microscopy (cryo- EM) measurement, called a micrograph, consists of multiple two-dimensional tomographic projections of a three-dimensional (3-D) molecular structure at unknown locations, taken under unknown viewing directions. A...")

05:1205:12, 24 August 2026 2026Jain ProtAcid (hist | edit) [1,760 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Jain, A., Cao, K. and Kihara, D. 2026. Computational approaches for protein–DNA/RNA complex modeling for Cryo-EM maps. Current Protocols. 6, 8 (2026), e70409. == Abstract == Cryogenic electron microscopy (cryo-EM) has become a key method in structural biology for determining macromolecular structures. Numerous computational tools have been developed to build atomic models from cryo-EM density maps. However, relatively few tools are available for model...")

05:3705:37, 21 August 2026 2025Schafer CryoSift (hist | edit) [1,146 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Schäfer, J.-H., Calza, A., Hom, K., Damodar, P., Peng, R., Bogdanović, N., Lander, G.C., Stagg, S.M. and Cianfrocco, M.A. 2025. CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection. Acta Crystallographica Sec. F. 81, 12 (2025), 517–526. == Abstract == Single-particle cryo-electron microscopy (cryo-EM) has become an essential tool in structural biology. However, automating repetitive tasks remains an ongoing challenge...")
05:2905:29, 21 August 2026 2025Shugaeva Prior (hist | edit) [1,801 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Shugaeva, T., Howard, R.J., Haloi, N. and Lindahl, E. 2025. Modeling cryo-EM structures in alternative states with AlphaFold2-based models and density-guided simulations. Communications Chemistry. 8, 1 (2025), 317. == Abstract == Modeling atomic coordinates into a target cryo-electron microscopy map is a crucial step in structure determination. Despite recent advances, proteins with multiple functional states remain a challenge - particularly when suita...")
05:2105:21, 21 August 2026 2025Zhang Struct2MapGAN (hist | edit) [1,465 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Zhang, C., Condon, A. and Dao Duc, K. 2025. Struc2mapGAN: improving synthetic cryogenic electron microscopy density maps with generative adversarial networks. Bioinformatics advances. 5, 1 (2025), vbaf179. == Abstract == Motivation Generating synthetic cryogenic electron microscopy 3D density maps from molecular structures has potential important applications in structural biology. Yet existing simulation-based methods cannot mimic all the complex featu...")
05:1105:11, 21 August 2026 2026Wankowicz Atomic (hist | edit) [1,555 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Wankowicz, S.A. and Bonomi, M. 2026. From possibility to precision in macromolecular ensemble prediction. Nature Methods. (2026), 1–9. == Abstract == Proteins and other macromolecules exist as dynamic ensembles of interconverting conformations essential for catalysis, allosteric regulation and molecular recognition. While AI tools like AlphaFold have revolutionized static structure prediction, they cannot yet capture conformational ensembles. Progress...")

08:5308:53, 20 August 2026 2022Dickerson InelasticContribution (hist | edit) [1,822 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Dickerson, J.L. and Russo, C.J. 2022. Phase contrast imaging with inelastically scattered electrons from any layer of a thick specimen. Ultramicroscopy. 237, (2022), 113511. == Abstract == A controversy exists as to whether the signal in a high resolution phase contrast electron micrograph of a particle in a thick specimen is the same irrespective of the particle’s position along the beam axis. Different conceptions of inelastic scattering and its eff...")
05:1205:12, 20 August 2026 2026Fadini Rocket (hist | edit) [1,866 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Fadini, A., Li, M., McCoy, A.J., Banjara, S., Okumura, H., Napier, E., Fontana, P., Khan, A.R., Jovine, L., Terwilliger, T.C. and others 2026. AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network. Nature methods. 23, (2026), 785–795. == Abstract == Advances in machine learning have transformed structural biology, enabling swift and accurate prediction of protein structure from sequence. However, key cha...")

06:3706:37, 13 August 2026 2025Gyawali Multimodal (hist | edit) [1,700 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Gyawali, R., Dhakal, A. and Cheng, J. 2025. Multimodal deep learning integration of cryo-EM and AlphaFold3 for high-accuracy protein structure determination. Communications Chemistry. 8, 1 (2025), 320. == Abstract == Cryo-electron microscopy (cryo-EM) is a key technology for determining the structures of proteins, particularly large protein complexes. However, automatically building high-accuracy protein structures from cryo-EM density maps remains a cr...")
06:3206:32, 13 August 2026 2026Savas Distogram (hist | edit) [1,113 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Savaş, B., Barlas, A.B. and Karaca, E. 2026. Exploring the potential of AlphaFold distograms for predicting binding-induced hinge motions. FEBS letters. 600, 10 (2026), 1558–1570. == Abstract == AlphaFold models provide static structural predictions, limiting their use in interpreting flexible regions in low-resolution cryo-EM maps. Here, we assess whether AlphaFold-generated distograms can instead reveal conformational flexibility, focusing on bindi...")
06:2506:25, 13 August 2026 2025Alexadrescu Mix (hist | edit) [1,831 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Alexandrescu, L., Lessin, W. and Lander, G.C. 2025. Mix-it-up’: accessible time-resolved cryo-EM on the millisecond timescale. IUCrJ. 12, 6 (2025), 710–724. == Abstract == Biological reactions often involve macromolecules that undergo substrate-induced conformational changes in under a second, yet capturing these transient states remains challenging. While high-resolution structural techniques such as X-ray crystallography and cryo-electron microsco...")
06:1806:18, 13 August 2026 2025Toader SGD (hist | edit) [1,984 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Toader, B., Brubaker, M.A. and Lederman, R.R. 2025. Efficient high-resolution refinement in cryo-EM with stochastic gradient descent. Acta Crystallographica Sec. D. 81, (2025), 327–343. == Abstract == Electron cryo-microscopy (cryo-EM) is an imaging technique that is widely used in structural biology to determine the three-dimensional structure of biological molecules from noisy two-dimensional projections with unknown orientations. As the typical pip...")
06:1106:11, 13 August 2026 2026Balanov Confirmation (hist | edit) [2,052 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Balanov, A., Huleihel, W. and Bendory, T. 2026. Einstein from noise: Statistical analysis. IEEE Transactions on Signal Processing. 74, (2026), 1751–1766. == Abstract == “Einstein from noise” (EfN) is a prominent example of the model bias phenomenon, where systematic errors in the statistical model lead to spurious but consistent estimates. In the EfN experiment, one falsely believes that a set of observations contains noisy, shifted copies of a te...")

04:3604:36, 12 August 2026 2025Zhang CryoFastAR (hist | edit) [1,836 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Zhang, J., Zhou, S., Dai, H., Liu, X., Wang, P., Fan, Z., Pei, Y. and Yu, J. 2025. CryoFastAR: Fast Cryo-EM Ab Initio Reconstruction Made Easy. 2025 IEEE/CVF International Conference on Computer Vision (ICCV) (2025), 8462–8471. == Abstract == Pose estimation from unordered images is fundamental for 3D reconstruction, robotics, and scientific imaging. Recent geometric foundation models, such as DUSt3R, enable end-to-end dense 3D reconstruction but rema...")
04:1904:19, 12 August 2026 2026Balanov Einstein (hist | edit) [2,052 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Balanov, A., Huleihel, W. and Bendory, T. 2026. Einstein from noise: Statistical analysis. IEEE Transactions on Signal Processing. 74, (2026), 1751–1766. == Abstract == “Einstein from noise” (EfN) is a prominent example of the model bias phenomenon, where systematic errors in the statistical model lead to spurious but consistent estimates. In the EfN experiment, one falsely believes that a set of observations contains noisy, shifted copies of a te...")

05:2805:28, 11 August 2026 2026Fromm LowDose (hist | edit) [2,369 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Fromm, S.A. and Mattei, S. 2026. LowDoseWizard–rapid and standardised setup of low-dose cryo-TEM imaging in SerialEM. Acta Crystallographica Sec. D. 82, (2026), 990–997. == Abstract == Structure elucidation of biological macromolecules by single-particle cryogenic electron microscopy (SPA cryo-EM) or cryogenic electron tomography (cryo- ET) relies on low-dose imaging on cryogenic transmission electron microscopes (cryo-TEMs). Routine microscope setu...")

05:1305:13, 10 August 2026 2026Marchan Unattended (hist | edit) [2,350 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Marchán Torres, D., Conesa, P., Garcia, A., Iceta, M., Broche, L., Gragera, M., Linares, R., Kwong, H.S., Chichón, F.J., Svensson, O. and others 2026. An unattended image-processing pipeline for on-the-fly quality assessment and 3D exploration in cryo-EM. Acta Crystallographica Sec. D. 82, 8 (2026). == Abstract == Single-particle analysis (SPA) by cryogenic electron microscopy (cryo-EM) has become a cornerstone of structural biology; yet, the workflow...")

11:0811:08, 7 August 2026 2026Van Polar (hist | edit) [1,827 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Van, C.T., Reboul, C.F., Caesar, J.J., Meana-Pañeda, R. and Elmlund, H. 2026. A polar Fourier geometric approach to volume-free single-particle 3D reconstruction. IUCrJ. 13, 4 (2026). == Abstract == We introduce a compact mathematical formulation for the inverse singleparticle 3D reconstruction problem, a high-dimensional inverse problem in which millions of parameters are estimated from extremely noisy experimental measurements. Given a collection of...")

06:3106:31, 23 July 2026 2013Ruskin DQE (hist | edit) [1,350 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Ruskin, A.I., Yu, Z. and Grigorieff, N. 2013. Quantitative characterization of electron detectors for transmission electron microscopy. J. Structural biology. 184, 3 (2013), 385–393. == Abstract == A new generation of direct electron detectors for transmission electron microscopy (TEM) promises significant improvement over previous detectors in terms of their modulation transfer function (MTF) and detective quantum efficiency (DQE). However, the perfo...")
06:1906:19, 23 July 2026 2026Motta Dublins (hist | edit) [979 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Motta Alves, G., Andrews, T., McBean, P., Wells, T., El-Gomati, M.M., Burkhalter, S., Schulze-Briese, C., Zambon, P., McMullan, G., Henderson, R. and others 2026. The Dublin lens: a Cc= 1.0 mm objective lens intended for CryoEM at 100 keV. Methods in Microscopy. 3, 1 (2026), 19–25. == Abstract == We have designed, fabricated and tested a lens with a chromatic aberration coefficient (Cc) of 1.0 mm, a 4.0 mm pole-gap and 2.0 mm bore that is wide enough...")

06:4606:46, 22 July 2026 2024Wang CryoSeek (hist | edit) [1,782 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Wang, T., Li, Z., Xu, K., Huang, W., Huang, G., Zhang, Q.C. and Yan, N. 2024. CryoSeek: A strategy for bioentity discovery using cryoelectron microscopy. Proceedings of the National Academy of Sciences. 121, 42 (2024), e2417046121. == Abstract == Structural biology is experiencing a paradigm shift from targeted structural determination to structure-guided discovery of previously uncharacterized bioentities. We employed cryoelectron microscopy (cryo-EM)...")

06:4306:43, 9 July 2026 2026Petrov Laser (hist | edit) [1,309 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Petrov, P.N., Zhang, J.T., Remis, J., Axelrod, J.J., Cheng, H., Cooper, E.S., Hicklin, I.K., Sandhaus, S., Schnurr, C., Glaeser, R.M. and others 2026. Laser phase plate improves structure determination of small proteins by cryo-EM. Science. (2026), eaeh0665. == Abstract == Phase plates can in principle overcome the poor image contrast in electron cryo–microscopy (cryo-EM) and the resulting limits on the structural reconstruction of small proteins. How...")
06:2406:24, 9 July 2026 2026Subramaniam Review (hist | edit) [1,201 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Subramaniam, S., Kühlbrandt, W. and Henderson, R. 2026. Cryo-EM: the revolution continues. IUCrJ. 13, 4 (2026). == Abstract == The near-universal adoption of electron cryo-microscopy (cryo-EM) by structural and cell biologists has led to exponential growth of the field, especially over the last two decades, with a doubling in the number of deposited electronmicroscopy density maps every 2.5 years. This exponential growth has changed in recent years to...")

06:3106:31, 7 July 2026 2026Chrencik SBDD (hist | edit) [1,648 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Chrencik, J.E., Su, H.-P., Gomez Llorente, Y., Palte, R.L., Klein, D.J., Hayes, R.P., Antine, S.P., Asmar-Rovira, G.A., Bertoletti, N., Byrne, N.J. and others 2026. The evolving role of structural biology in pharma: integration of X-ray crystallography, cryo-electron microscopy and beyond. Biological Crystallography. 82, 6 (2026). == Abstract == Structural biology has fundamentally influenced pharmaceutical research and development at Merck Sharp & Dohm...")
06:1706:17, 7 July 2026 2025Starynska Membrane (hist | edit) [1,461 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Starynska, A., Cameron, C.J., Sigworth, F.J. and Tagare, H.D. 2026. Automated Membrane Detection and Subtraction for Structure Determination of Membrane Proteins in Cryogenic Electron Microscopy. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (2026), 6553–6562. == Abstract == High-resolution cryo-electron microscopy (cryo-EM) reconstruction of membrane proteins often requires the bilayer membrane containing the prote...")
05:5505:55, 7 July 2026 2026Gao CryoKRAQEN (hist | edit) [1,599 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Gao, W., Wu, Y. and He, X. 2026. CryoKRAQEN: Kernel-Regularized Annealing for Quantized Embedding Networks in Cryo-EM Heterogeneous Reconstruction. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (2026), 28298–28307. == Abstract == Heterogeneous reconstruction in cryo-electron microscopy (Cryo-EM) is fundamental for understanding macromolecular structural diversity, yet remains challenging due to extreme noise, contin...")

06:5806:58, 2 June 2026 2026Behkamal Secondary (hist | edit) [2,958 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Behkamal, B., Etemadheravi, M.P., Mahmoodjanloo, A., Mansoori, A., Naghibzadeh, M., Al Nasr, K. and Saberi, M.R. 2026. A Novel Machine-Learning Based Method for Resolving Secondary Structure Topology in Medium-Resolution Cryo-EM Density Maps. Intl. J. of Molecular Sciences. 27, 10 (2026), 4388. == Abstract == Medium-resolution cryo-electron microscopy (cryo-EM) density maps preserve substantial information about protein secondary-structure organization;...")
06:1606:16, 2 June 2026 2026Kwon Elastic (hist | edit) [1,218 bytes] WikiSysop (talk | contribs) (Created page with "== Citation == Kwon, M.C. and Abrahams, J.P. 2026. Elastic and Inelastic Interactions of Electrons in Transmission Electron Microscopy. Ultramicroscopy. (2026), 114383. == Abstract == High-energy electrons passing through a sample in a transmission electron microscope carry structural information through their interactions with the sample’s atoms. Elastically scattered electrons, which undergo no significant energy loss, convey spatial details in their scattering an...")

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