ArticleBioinformatics (Oxford, England)2024
RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 142 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
142 citing papers in PubMed.
- Formate as electron carrier in the gut acetogenGut microbes · 2026Article
- Adaptive deletion of functional duplicate genes in Drosophila.Journal of evolutionary biology · 2026Article
- An ancient evolutionary origin for IL-1 cytokines.Nature ecology & evolution · 2026Article
- Structural basis of IgLON5 autoantibody recognition in autoimmune encephalitis.Nature communications · 2026Article
- Dual roles of genes required for intrinsic resistance to clarithromycin in evasion of killing by serum complement inInfection and immunity · 2026Article
- Conserved mRNP remodeling mechanism of the TREX-2.1 complex.Nucleic acids research · 2026Article
- Article
- Toward an Understanding of the Mechanistic Differences Between the Hydroxylating and Desaturating Pyridoxal 5'-Phosphate-Dependent L-Arginine Oxidases.Chembiochem : a European journal of chemical biology · 2026Article
- Development of a Nanoscale Protein-Protein Mapping of PDE4 Interface-Disrupting Peptides.Nano letters · 2026Article
- Structural Diversity and Differential Natural Pairings of MAT1-1-1 and MAT1-2-1 Proteins Essential for Sexual Reproduction inInternational journal of molecular sciences · 2026Article
- Barley HvBODYGUARD1 controls cuticular specialisations regulated by SHINE transcription factors.The New phytologist · 2026Article
- Evolutionary relationship between yeast telomeric protein Cdc13 and Pot1.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Article
- CRISPR-Cas9 mediated knockout of the white gene in the bluetongue virus vector, Culicoides sonorensis (biting midge).Scientific reports · 2026Article
- Tracing the origins of crmA megasynthase through lichen genomes.Current biology : CB · 2026Article
- A conserved mechanism for dimerization and activation of superfamily 1A UvrD-family helicases.Nucleic acids research · 2026Article
- The vesicular stomatitis virus matrix protein promotes FACT subunit depletion to suppress the FEAR pathway.PLoS pathogens · 2026Article
- Engineered B7-H3 Binding in Modular Gp2 Miniproteins.Biotechnology and bioengineering · 2026Article
- The Trichinella Super-Pangenome Reveals the Evolution of Encapsulation and Predicted Host-Parasite Protein Interactions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Review
- RGS22 is a metazoa-specific radial spoke component required for coordinated ciliary beating.Nature communications · 2026Article
82 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
motivationTools for pairwise alignments between 3D structures of proteins are of fundamental importance for structural biology and bioinformatics, enabling visual exploration of evolutionary and functional relationships. However, the absence of a user-friendly, browser-based tool for creating alignments and visualizing them at both 1D sequence and 3D structural levels makes this process unnecessarily cumbersome.
resultsWe introduce a novel pairwise structure alignment tool (rcsb.org/alignment) that seamlessly integrates into the RCSB Protein Data Bank (RCSB PDB) research-focused RCSB.org web portal. Our tool and its underlying application programming interface (alignment.rcsb.org) empowers users to align several protein chains with a reference structure by providing access to established alignment algorithms (FATCAT, CE, TM-align, or Smith-Waterman 3D). The user-friendly interface simplifies parameter setup and input selection. Within seconds, our tool enables visualization of results in both sequence (1D) and structural (3D) perspectives through the RCSB PDB RCSB.org Sequence Annotations viewer and Mol* 3D viewer, respectively. Users can effortlessly compare structures deposited in the PDB archive alongside more than a million incorporated Computed Structure Models coming from the ModelArchive and AlphaFold DB. Moreover, this tool can be used to align custom structure data by providing a link/URL or uploading atomic coordinate files directly. Importantly, alignment results can be bookmarked and shared with collaborators. By bridging the gap between 1D sequence and 3D structures of proteins, our tool facilitates deeper understanding of complex evolutionary relationships among proteins through comprehensive sequence and structural analyses. AVAILABILITY AND IMPLEMENTATION: The alignment tool is part of the RCSB PDB research-focused RCSB.org web portal and available at rcsb.org/alignment. Programmatic access is available via alignment.rcsb.org. Frontend code has been published at github.com/rcsb/rcsb-pecos-app. Visualization is powered by the open-source Mol* viewer (github.com/molstar/molstar and github.com/molstar/rcsb-molstar) plus the Sequence Annotations in 3D Viewer (github.com/rcsb/rcsb-saguaro-3d).
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.