ArticleCommunications biology2022
Real-time structure search and structure classification for AlphaFold protein models.
Article in Communications biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Benchmarking protein sequence and structure search methods for remote homology detection.Genome biology · 2026Article
- PL-PatchSurfer3: improved structure-based virtual screening for structure variation using 3D Zernike descriptors.Journal of cheminformatics · 2026Article
- AI accelerate the identification of druggable targets by 3D structures of proteins and compounds.NPJ precision oncology · 2026Review
- Modern resources for intrinsic disorder predictions: protein language models, deep learning, meta-servers, and databases.Cellular and molecular life sciences : CMLS · 2026Review
- SHREC 2025: Protein surface shape retrieval including electrostatic potential.Computers & graphics · 2025Article
- Article
- Controlled liquid-liquid phase separation via the simulation-guided, targeted engineering of the RNA-binding protein PARCL.iScience · 2025Article
- Enhancing the Thermostability ofMolecules (Basel, Switzerland) · 2025Article
- An outlook on structural biology after AlphaFold: tools, limits and perspectives.FEBS open bio · 2025Review
- Fast protein structure searching using structure graph embeddings.Bioinformatics advances · 2025Article
- PS-GO parametric protein search engine.Computational and structural biotechnology journal · 2024Article
- Cationic Surface Charge Engineering of Recombinant Transthyretin Remarkably Increases the Inhibitory Potency Against Amyloid β-Protein Fibrillogenesis.Molecules (Basel, Switzerland) · 2024Article
- DEGRONOPEDIA: a web server for proteome-wide inspection of degrons.Nucleic acids research · 2024Article
- FP-Zernike: An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval.Genomics, proteomics & bioinformatics · 2024Article
- Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints.Journal of molecular biology · 2024Article
- Recent Progress of Protein Tertiary Structure Prediction.Molecules (Basel, Switzerland) · 2024Review
- ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration.Bioinformatics advances · 2024Article
- Structural Outlier Detection and Zernike-Canterakis Moments for Molecular Surface Meshes-Fast Implementation in Python.Molecules (Basel, Switzerland) · 2023Article
- Is Protein BLAST a thing of the past?Nature communications · 2023Article
- Assembly of Protein Complexes In and On the Membrane with Predicted Spatial Arrangement Constraints.bioRxiv : the preprint server for biology · 2023Article
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Authors and funding
8 authors.
Funding
Abstract
Last year saw a breakthrough in protein structure prediction, where the AlphaFold2 method showed a substantial improvement in the modeling accuracy. Following the software release of AlphaFold2, predicted structures by AlphaFold2 for proteins in 21 species were made publicly available via the AlphaFold Database. Here, to facilitate structural analysis and application of AlphaFold2 models, we provide the infrastructure, 3D-AF-Surfer, which allows real-time structure-based search for the AlphaFold2 models. In 3D-AF-Surfer, structures are represented with 3D Zernike descriptors (3DZD), which is a rotationally invariant, mathematical representation of 3D shapes. We developed a neural network that takes 3DZDs of proteins as input and retrieves proteins of the same fold more accurately than direct comparison of 3DZDs. Using 3D-AF-Surfer, we report structure classifications of AlphaFold2 models and discuss the correlation between confidence levels of AlphaFold2 models and intrinsic disordered regions.
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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.