ArticleBioinformatics (Oxford, England)2025
AlphaPulldown2-a general pipeline for high-throughput structural modeling.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed.
- AlphaFold reveals how pathogenicmBio · 2026Article
- Evolutionary analysis of transcription elongation factors reveals conserved and lineage-specific regulatory domains.PLoS biology · 2026Article
- The bacterial swarming factor SwrD forms hexameric rings reminiscent of DNA-binding proteins.bioRxiv : the preprint server for biology · 2026Article
- Deciphering Membrane Protein Complexes in Plasmodium falciparum Gametocytes via Integrative Structural Systems Biology.Molecular & cellular proteomics : MCP · 2026Article
- The PER2:BRCA1:POU2F1(OCT-1) ternary complex represents a multi-component scaffold model for circadian gene regulation.Neurobiology of sleep and circadian rhythms · 2026Article
- Advances and opportunities for computational interrogation of plant proteins.The Plant journal : for cell and molecular biology · 2026Review
- AlphaFold-driven discovery of oxysterol-binding protein-related protein-phosphoinositide 3-, 4-, and 5-phosphatase interactions using new generation confidence scores.Protein science : a publication of the Protein Society · 2026Article
- Guiding AlphaFold predictions with experimental knowledge to inform dynamics and interactions with VAIRO.Protein science : a publication of the Protein Society · 2026Article
- Evolutionary conservation and innovations of RNA polymerase II transcription elongation factors.bioRxiv : the preprint server for biology · 2026Article
- Adversarial Sequence Mutations in AlphaFold and ESMFold Reveal Nonphysical Structural Invariance, Confidence Failures, and Concerns for Protein Design.Computational and structural biotechnology journal · 2026Article
- gapTrick-structural characterization of protein-protein interactions using AlphaFold.Bioinformatics (Oxford, England) · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
summaryAlphaPulldown2 streamlines protein structural modeling by automating workflows, improving code adaptability, and optimizing data management for large-scale applications. It introduces an automated Snakemake pipeline, compressed data storage, support for additional modeling backends like UniFold and AlphaLink2, and a range of other improvements. These upgrades make AlphaPulldown2 a versatile platform for predicting both binary interactions and complex multi-unit assemblies. AVAILABILITY AND IMPLEMENTATION: AlphaPulldown2 is freely available at https://github.com/KosinskiLab/AlphaPulldown.
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.