ReviewBiophysical reviews2022
Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future.
Review in Biophysical reviews, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
33 citing papers in PubMed, 45 citations in OpenAlex.
- Predicting water at the protein interface in cryo-EM structures from MD-excess chemical potential.Biophysical journal · 2026Article
- KNexPHENIX: A PHENIX-Based Workflow for Improving Cryo-EM and Crystallographic Structural Models.Journal of chemical information and modeling · 2026Article
- Calculating Enzyme Inhibition with Random Forests.Methods in molecular biology (Clifton, N.J.) · 2026Article
- MetaMP Ecosystem for Unified, Auditable, and Benchmark-Ready Data for Reliable Membrane Protein Annotation.Computational and structural biotechnology journal · 2026Article
- Gradient Descent to Predict Enzyme Inhibition.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Decision Tree for Prediction of Binding Affinity.Methods in molecular biology (Clifton, N.J.) · 2026Article
- KNexPHENIX: A PHENIX-Based Workflow for Improving Cryo-EM and Crystallographic Structural Models.bioRxiv : the preprint server for biology · 2025Article
- Cryo-EM reveals molecular mechanisms underlying the inhibitory effect of netrin-4 on laminin matrix formation.Nature communications · 2025Article
- Q-score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps.Acta crystallographica. Section D, Structural biology · 2025Article
- Subtle Changes at the RBD/hACE2 Interface During SARS-CoV-2 Variant Evolution: A Molecular Dynamics Study.Biomolecules · 2025Article
- A new chapter for RCSB Protein Data Bank Molecule of the Month in 2025.Structural dynamics (Melville, N.Y.) · 2025Article
- Wiener filter unifies Hilbert and Zernike phase plates in electron microscopy.Biophysical reviews · 2025Review
- Ligand identification in CryoEM and X-ray maps using deep learning.Bioinformatics (Oxford, England) · 2024Article
- Ligand Identification in CryoEM and X-ray Maps Using Deep Learning.bioRxiv : the preprint server for biology · 2024Article
- Cryo-Electron Microscopy Studies of Biomolecular Structure and Dynamics.Micromachines · 2024Article
- Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.Nature methods · 2024Article
- Article
- Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM.bioRxiv : the preprint server for biology · 2024Article
- MESPEUS: a database of metal coordination groups in proteins.Nucleic acids research · 2024Article
- The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids.Nucleic acids research · 2024Article
Corrections and comments
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Authors and funding
16 authors at 4 institutions in 1 country.
Funding
Abstract
As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) "Resolution Revolution" made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.