ArticleCurrent protocols in bioinformatics2017
Protein 3D Structure and Electron Microscopy Map Retrieval Using 3D-SURFER2.0 and EM-SURFER.
Article in Current protocols in bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 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
- CryoAlign2: efficient global and local Cryo-EM map retrieval based on parallel-accelerated local spatial structural features.Bioinformatics (Oxford, England) · 2025Article
- 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
- Classification of protein domains based on their three-dimensional shapes (CPD3DS).Synthetic and systems biotechnology · 2021Article
- VESPER: global and local cryo-EM map alignment using local density vectors.Nature communications · 2021Article
- A global map of the protein shape universe.PLoS computational biology · 2019Article
- Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery.Frontiers in chemistry · 2018Review
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Authors and funding
3 authors.
Funding
Abstract
With the rapid growth in the number of solved protein structures stored in the Protein Data Bank (PDB) and the Electron Microscopy Data Bank (EMDB), it is essential to develop tools to perform real-time structure similarity searches against the entire structure database. Since conventional structure alignment methods need to sample different orientations of proteins in the three-dimensional space, they are time consuming and unsuitable for rapid, real-time database searches. To this end, we have developed 3D-SURFER and EM-SURFER, which utilize 3D Zernike descriptors (3DZD) to conduct high-throughput protein structure comparison, visualization, and analysis. Taking an atomic structure or an electron microscopy map of a protein or a protein complex as input, the 3DZD of a query protein is computed and compared with the 3DZD of all other proteins in PDB or EMDB. In addition, local geometrical characteristics of a query protein can be analyzed using VisGrid and LIGSITE
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