ArticleBMC bioinformatics2015
Navigating 3D electron microscopy maps with EM-SURFER.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- PL-PatchSurfer3: improved structure-based virtual screening for structure variation using 3D Zernike descriptors.Journal of cheminformatics · 2026Article
- SHREC 2025: Protein surface shape retrieval including electrostatic potential.Computers & graphics · 2025Article
- Article
- Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints.Journal of molecular biology · 2024Article
- Assembly of Protein Complexes In and On the Membrane with Predicted Spatial Arrangement Constraints.bioRxiv : the preprint server for biology · 2023Article
- Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches.Frontiers in molecular biosciences · 2023Article
- ContactPFP: Protein function prediction using predicted contact information.Frontiers in bioinformatics · 2022Article
- Surface-based protein domains retrieval methods from a SHREC2021 challenge.Journal of molecular graphics & modelling · 2022Article
- VESPER: global and local cryo-EM map alignment using local density vectors.Nature communications · 2021Article
- FTIP: an accurate and efficient method for global protein surface comparison.Bioinformatics (Oxford, England) · 2020Article
- Predicting binding poses and affinity ranking in D3R Grand Challenge using PL-PatchSurfer2.0.Journal of computer-aided molecular design · 2019Article
- Searching for 3D structural models from a library of biological shapes using a few 2D experimental images.BMC bioinformatics · 2018Article
- Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery.Frontiers in chemistry · 2018Review
- Protein 3D Structure and Electron Microscopy Map Retrieval Using 3D-SURFER2.0 and EM-SURFER.Current protocols in bioinformatics · 2017Article
- PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation.Journal of chemical information and modeling · 2016Article
- Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB.Bioinformatics (Oxford, England) · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundThe Electron Microscopy DataBank (EMDB) is growing rapidly, accumulating biological structural data obtained mainly by electron microscopy and tomography, which are emerging techniques for determining large biomolecular complex and subcellular structures. Together with the Protein Data Bank (PDB), EMDB is becoming a fundamental resource of the tertiary structures of biological macromolecules. To take full advantage of this indispensable resource, the ability to search the database by structural similarity is essential. However, unlike high-resolution structures stored in PDB, methods for comparing low-resolution electron microscopy (EM) density maps in EMDB are not well established.
resultsWe developed a computational method for efficiently searching low-resolution EM maps. The method uses a compact fingerprint representation of EM maps based on the 3D Zernike descriptor, which is derived from a mathematical series expansion for EM maps that are considered as 3D functions. The method is implemented in a web server named EM-SURFER, which allows users to search against the entire EMDB in real-time. EM-SURFER compares the global shapes of EM maps. Examples of search results from different types of query structures are discussed.
conclusionsWe developed EM-SURFER, which retrieves structurally relevant matches for query EM maps from EMDB within seconds. The unique capability of EM-SURFER to detect 3D shape similarity of low-resolution EM maps should prove invaluable in structural biology.
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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.