ArticleProteins2015
Manual classification strategies in the ECOD database.
Article in Proteins, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
52 citing papers in PubMed.
- The history of enzyme evolution embedded in metabolism.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Evaluating the evolutionary relationship of TATA binding protein (TBP) with various folding patterns of protein domains using support vector machine (SVM).Scientific reports · 2026Article
- Assessing Structural Classification Using AlphaFold2 Models Through ECOD-Based Comparative Analysis.Proteins · 2025Article
- Distribution of Polyphosphate Kinase 2 Genes in Bacteria Underscores a Dynamic Evolutionary History.Proteins · 2025Article
- IgStrand: A universal residue numbering scheme for the immunoglobulin-fold (Ig-fold) to study Ig-proteomes and Ig-interactomes.PLoS computational biology · 2025Review
- Refinement and curation of homologous groups facilitated by structure prediction.Protein science : a publication of the Protein Society · 2025Article
- Ig or Not Ig? That Is the Question: The Nucleating Supersecondary Structure of the Ig-Fold and the Extended Ig Universe.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Structural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts.PLoS computational biology · 2024Article
- DDMut-PPI: predicting effects of mutations on protein-protein interactions using graph-based deep learning.Nucleic acids research · 2024Article
- Primitive purine biosynthesis connects ancient geochemistry to modern metabolism.Nature ecology & evolution · 2024Article
- ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2.PLoS computational biology · 2024Article
- Insights into virulence: structure classification of themSystems · 2023Article
- Conservation of knotted and slipknotted topology in transmembrane transporters.Biophysical journal · 2023Article
- Retracing the evolution of a modern periplasmic binding protein.Protein science : a publication of the Protein Society · 2023Article
- PyProtif: a PyMol plugin to retrieve and visualize protein motifs for structural studies.Amino acids · 2023Article
- Classification of domains in predicted structures of the human proteome.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning.Nucleic acids research · 2023Article
- An evolutionary history of the CoA-binding protein Nat/Ivy.Protein science : a publication of the Protein Society · 2022Review
- RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.Protein science : a publication of the Protein Society · 2022Article
- Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students.Biomolecules · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
ECOD (Evolutionary Classification Of protein Domains) is a comprehensive and up-to-date protein structure classification database. The majority of new structures released from the PDB (Protein Data Bank) each week already have close homologs in the ECOD hierarchy and thus can be reliably partitioned into domains and classified by software without manual intervention. However, those proteins that lack confidently detectable homologs require careful analysis by experts. Although many bioinformatics resources rely on expert curation to some degree, specific examples of how this curation occurs and in what cases it is necessary are not always described. Here, we illustrate the manual classification strategy in ECOD by example, focusing on two major issues in protein classification: domain partitioning and the relationship between homology and similarity scores. Most examples show recently released and manually classified PDB structures. We discuss multi-domain proteins, discordance between sequence and structural similarities, difficulties with assessing homology with scores, and integral membrane proteins homologous to soluble proteins. By timely assimilation of newly available structures into its hierarchy, ECOD strives to provide a most accurate and updated view of the protein structure world as a result of combined computational and expert-driven analysis.
Indexed as
Identifiers
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.