ArticleScientific reports2018
PANDA: Protein function prediction using domain architecture and affinity propagation.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed.
- Graph Learning in Bioinformatics: A Survey of Graph Neural Network Architectures, Biological Graph Construction and Bioinformatics Applications.Biomolecules · 2026Review
- Graph Neural Network-Based Approaches for Protein Function Prediction.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Tracing the function expansion for a primordial protein fold in the era of fold-based function prediction: β-trefoil.PloS one · 2025Article
- PANDA-3D: protein function prediction based on AlphaFold models.NAR genomics and bioinformatics · 2024Article
- PRONTO-TK: a user-friendly PROtein Neural neTwOrk tool-kit for accessible protein function prediction.NAR genomics and bioinformatics · 2024Article
- Review
- PANDA2: protein function prediction using graph neural networks.NAR genomics and bioinformatics · 2022Article
- DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web.Nucleic acids research · 2021Article
- Spontaneous Phage Resistance in Avian PathogenicFrontiers in microbiology · 2021Article
- Protein domain identification methods and online resources.Computational and structural biotechnology journal · 2021Review
- Article
- The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction.Bioinformatics (Oxford, England) · 2020Article
- Transcriptomic Prediction of PigGenes · 2020Article
- Cis- and trans-regulations of pre-mRNA splicing by RNA editing enzymes influence cancer development.Nature communications · 2020Article
- Predicting Sequence Features, Function, and Structure of Proteins Using MESSA.Current protocols in bioinformatics · 2019Article
- Article
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
We developed PANDA (Propagation of Affinity and Domain Architecture) to predict protein functions in the format of Gene Ontology (GO) terms. PANDA at first executes profile-profile alignment algorithm to search against PfamA, KOG, COG, and SwissProt databases, and then launches PSI-BLAST against UniProt for homologue search. PANDA integrates a domain architecture inference algorithm based on the Bayesian statistics that calculates the probability of having a GO term. All the candidate GO terms are pooled and filtered based on Z-score. After that, the remaining GO terms are clustered using an affinity propagation algorithm based on the GO directed acyclic graph, followed by a second round of filtering on the clusters of GO terms. We benchmarked the performance of all the baseline predictors PANDA integrates and also for every pooling and filtering step of PANDA. It can be found that PANDA achieves better performances in terms of area under the curve for precision and recall compared to the baseline predictors. PANDA can be accessed from http://dna.cs.miami.edu/PANDA/ .
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.