ArticlePLoS computational biology2020
Real time structural search of the Protein Data Bank.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers, 1 of them a synthesis that pooled it.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
47 citing papers in PubMed, 1 synthesis or guideline pooled it, 65 citations in OpenAlex.
- Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon.Communications biology · 2023Pooled it
- A sterol reductase responsible for the unusual 8(14)-unsaturation in bacterial sterol production and degradation.Journal of bacteriology · 2026Article
- A sterol reductase responsible for the unusual 8(14)-unsaturation in bacterial sterol production and degradation.bioRxiv : the preprint server for biology · 2026Article
- Multi-scale structural similarity embedding search across entire proteomes.Bioinformatics (Oxford, England) · 2026Article
- Predicting epistasis across proteins by structural logic.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Studying the Evolution of Protein Structure One Superfamily at a Time.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Immunogenicity of Adalimumab in Bacterial Molecular Mimicry: In Silico Analysis.JMIR bioinformatics and biotechnology · 2025Article
- Engineering Peptide Modulators for T-Cell Migration by Structural Scaffold Matching.Journal of medicinal chemistry · 2025Article
- Machine Learning Meets Physics-based Modeling: A Mass-spring System to Predict Protein-ligand Binding Affinity.Current medicinal chemistry · 2025Review
- Rapid and sensitive protein complex alignment with Foldseek-Multimer.Nature methods · 2025Article
- Fast protein structure searching using structure graph embeddings.Bioinformatics advances · 2025Article
- Advancements in Structural Basis of Covalent Inhibitors Targeting SARS-CoV-2 Essential Proteins.Current medicinal chemistry · 2025Review
- Why is binding of a divalent metal cation to a structural motif containing four carboxylate residues not accompanied by a conformational change?Protein science : a publication of the Protein Society · 2024Article
- PLO3S: Protein LOcal Surficial Similarity Screening.Computational and structural biotechnology journal · 2024Article
- FP-Zernike: An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval.Genomics, proteomics & bioinformatics · 2024Article
- Article
- Recent Advances in Protein Folding Pathway Prediction through Computational Methods.Current medicinal chemistry · 2024Review
- Moment-based metrics for molecules computable from cryogenic electron microscopy images.Biological imaging · 2024Article
- ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration.Bioinformatics advances · 2024Article
- Exploring Scoring Function Space: Developing Computational Models for Drug Discovery.Current medicinal chemistry · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Detection of protein structure similarity is a central challenge in structural bioinformatics. Comparisons are usually performed at the polypeptide chain level, however the functional form of a protein within the cell is often an oligomer. This fact, together with recent growth of oligomeric structures in the Protein Data Bank (PDB), demands more efficient approaches to oligomeric assembly alignment/retrieval. Traditional methods use atom level information, which can be complicated by the presence of topological permutations within a polypeptide chain and/or subunit rearrangements. These challenges can be overcome by comparing electron density volumes directly. But, brute force alignment of 3D data is a compute intensive search problem. We developed a 3D Zernike moment normalization procedure to orient electron density volumes and assess similarity with unprecedented speed. Similarity searching with this approach enables real-time retrieval of proteins/protein assemblies resembling a target, from PDB or user input, together with resulting alignments (http://shape.rcsb.org).
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What OpenQuestion holds
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.