ArticleStructure (London, England : 1993)2022
Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level.
Article in Structure (London, England : 1993), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 42 citations in OpenAlex.
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- The p.(Leu97Ile) variant expands the genetic landscape of NEFL-associated Charcot-Marie-tooth neuropathies.Human molecular genetics · 2026Article
- Drug target mining and in silico screening of Tibetan plant metabolites for potential alleviation of Oroya fever, a neglected tropical disease.Scientific reports · 2026Article
- Structural analysis of uridine modifications in solved RNA structures.NAR genomics and bioinformatics · 2026Article
- Multi-scale structural similarity embedding search across entire proteomes.Bioinformatics (Oxford, England) · 2026Article
- Artificial intelligence-guided discovery of a lead compound with antifolate-like activity against bacterial and human thymidylate synthases.Frontiers in cellular and infection microbiology · 2026Article
- From CASP13 to the Nobel Prize: DeepMind's AlphaFold Journey in Revolutionizing Protein Structure Prediction and Beyond.Current protein & peptide science · 2026Review
- gapTrick-structural characterization of protein-protein interactions using AlphaFold.Bioinformatics (Oxford, England) · 2025Article
- Article
- Aromatic Residue Variations in the Central β‑Sheet Influence Stability and Activity of E. coli Glutaredoxin 3.ACS omega · 2025Article
- PDBrestore: A Free Web Interface for Processing and Fixing Protein Chains From Raw PDB Files.Journal of computational chemistry · 2025Article
- Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments.bioRxiv : the preprint server for biology · 2025Article
- Deciphering the Regulatory Potential of Antioxidant and Electron-Shuttling Bioactive Compounds in Oolong Tea.Biology · 2025Article
- Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study.Protein science : a publication of the Protein Society · 2025Article
- Bridging prediction and reality: Comprehensive analysis of experimental and AlphaFold 2 full-length nuclear receptor structures.Computational and structural biotechnology journal · 2025Article
- Diversity, Distribution and Structural Prediction of the Pathogenic Bacterial Effectors EspN and EspS.Genes · 2024Article
- Benchmarking of AlphaFold2 accuracy self-estimates as indicators of empirical model quality and ranking: a comparison with independent model quality assessment programmes.Bioinformatics (Oxford, England) · 2024Article
- Article
- AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination.Nature methods · 2024Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Approximately 87% of the more than 190,000 atomic-level three-dimensional (3D) biostructures in the PDB were determined using macromolecular crystallography (MX). Agreement between 3D atomic coordinates and experimental data for >100 million individual amino acid residues occurring within ∼150,000 PDB MX structures was analyzed in detail. The real-space correlation coefficient (RSCC) calculated using the 3D atomic coordinates for each residue and experimental-data-derived electron density enables outlier detection of unreliable atomic coordinates (particularly important for poorly resolved side-chain atoms) and ready evaluation of local structure quality by PDB users. For human protein MX structures in PDB, comparisons of the per-residue RSCC metric with AlphaFold2-computed structure model confidence (pLDDT-predicted local distance difference test) document (1) that RSCC values and pLDDT scores are correlated (median correlation coefficient ∼0.41), and (2) that experimentally determined MX structures (3.5 Å resolution or better) are more reliable than AlphaFold2-computed structure models and should be used preferentially whenever possible.
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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.