ArticleNucleic acids research2006
Protein structure database search and evolutionary classification.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 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
57 citing papers in PubMed.
- Scalable homology detection with ERAST.Nature biotechnology · 2026Article
- A graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-align.Nature protocols · 2026Review
- SARST2 high-throughput and resource-efficient protein structure alignment against massive databases.Nature communications · 2025Article
- epLSAP-Align: a non-sequential protein structural alignment solver with entropy-regularized partial linear sum assignment problem formulation.Bioinformatics (Oxford, England) · 2025Article
- Complex structure and activation mechanism of arginine kinase McsB by McsA.Nature chemical biology · 2025Article
- An integrated structural and biophysical approach to study carbon metabolism inQRB discovery · 2025Review
- CATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets.Biology methods & protocols · 2025Article
- Protein structure alignment by Reseek improves sensitivity to remote homologs.Bioinformatics (Oxford, England) · 2024Article
- PLMSearch: Protein language model powers accurate and fast sequence search for remote homology.Nature communications · 2024Article
- Utilizing the scale-invariant feature transform algorithm to align distance matrices facilitates systematic protein structure comparison.Bioinformatics (Oxford, England) · 2024Article
- Fast and accurate protein structure search with Foldseek.Nature biotechnology · 2024Article
- SAFoldNet: A Novel Tool for Discovering and Aligning Three-Dimensional Protein Structures Based on a Neural Network.International journal of molecular sciences · 2023Article
- Novel machine learning approaches revolutionize protein knowledge.Trends in biochemical sciences · 2023Review
- Promiscuity of response regulators for thioredoxin steers bacterial virulence.Nature communications · 2022Article
- Article
- Structural and functional characterization of a putative de novo gene in Drosophila.Nature communications · 2021Article
- A secondary structure-based position-specific scoring matrix applied to the improvement in protein secondary structure prediction.PloS one · 2021Article
- Substrate-recognition mechanism of tomato β-galactosidase 4 using X-ray crystallography and docking simulation.Planta · 2020Article
- Ab initio folding of a trefoil-fold motif reveals structural similarity with a β-propeller blade motif.Protein science : a publication of the Protein Society · 2020Article
- PMP-diketopiperazine adducts form at the active site of a PLP dependent enzyme involved in formycin biosynthesis.Chemical communications (Cambridge, England) · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As more protein structures become available and structural genomics efforts provide structural models in a genome-wide strategy, there is a growing need for fast and accurate methods for discovering homologous proteins and evolutionary classifications of newly determined structures. We have developed 3D-BLAST, in part, to address these issues. 3D-BLAST is as fast as BLAST and calculates the statistical significance (E-value) of an alignment to indicate the reliability of the prediction. Using this method, we first identified 23 states of the structural alphabet that represent pattern profiles of the backbone fragments and then used them to represent protein structure databases as structural alphabet sequence databases (SADB). Our method enhanced BLAST as a search method, using a new structural alphabet substitution matrix (SASM) to find the longest common substructures with high-scoring structured segment pairs from an SADB database. Using personal computers with Intel Pentium4 (2.8 GHz) processors, our method searched more than 10 000 protein structures in 1.3 s and achieved a good agreement with search results from detailed structure alignment methods. [3D-BLAST is available at http://3d-blast.life.nctu.edu.tw].
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.