ArticleBMC bioinformatics2008
A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 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
34 citing papers in PubMed, 55 citations in OpenAlex.
- Training bias and sequence alignments shape protein-peptide docking by AlphaFold and related methods.Protein science : a publication of the Protein Society · 2025Article
- Easy triplex: An online tool for predicting the formation of DNA-RNA triple helices.Computational and structural biotechnology journal · 2025Article
- PairK: Pairwise k-mer alignment for quantifying protein motif conservation in disordered regions.Protein science : a publication of the Protein Society · 2025Article
- PairK: Pairwise k-mer alignment for quantifying protein motif conservation in disordered regions.bioRxiv : the preprint server for biology · 2024Article
- Fast and scalable querying of eukaryotic linear motifs with gget elm.Bioinformatics (Oxford, England) · 2024Article
- Computational analysis of the evolutionarily conserved Missing In Metastasis/Metastasis Suppressor 1 gene predicts novel interactions, regulatory regions and transcriptional control.Scientific reports · 2019Article
- Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks.Scientific reports · 2017Article
- SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions.Nucleic acids research · 2017Article
- Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad.Cell communication and signaling : CCS · 2015Review
- Natural variability of minimotifs in 1092 people indicates that minimotifs are targets of evolution.Nucleic acids research · 2015Article
- Predicting peptide-mediated interactions on a genome-wide scale.PLoS computational biology · 2015Article
- Classification of intrinsically disordered regions and proteins.Chemical reviews · 2014Review
- SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions.Nucleic acids research · 2012Article
- Deciphering a global network of functionally associated post-translational modifications.Molecular systems biology · 2012Article
- iELM--a web server to explore short linear motif-mediated interactions.Nucleic acids research · 2012Article
- The identification of short linear motif-mediated interfaces within the human interactome.Bioinformatics (Oxford, England) · 2012Article
- Proteome-wide discovery of evolutionary conserved sequences in disordered regions.Science signaling · 2012Article
- ELM--the database of eukaryotic linear motifs.Nucleic acids research · 2012Article
- A dynamic view of domain-motif interactions.PLoS computational biology · 2012Article
- SLiMSearch 2.0: biological context for short linear motifs in proteins.Nucleic acids research · 2011Article
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 at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe structure of many eukaryotic cell regulatory proteins is highly modular. They are assembled from globular domains, segments of natively disordered polypeptides and short linear motifs. The latter are involved in protein interactions and formation of regulatory complexes. The function of such proteins, which may be difficult to define, is the aggregate of the subfunctions of the modules. It is therefore desirable to efficiently predict linear motifs with some degree of accuracy, yet sequence database searches return results that are not significant.
resultsWe have developed a method for scoring the conservation of linear motif instances. It requires only primary sequence-derived information (e.g. multiple alignment and sequence tree) and takes into account the degenerate nature of linear motif patterns. On our benchmarking, the method accurately scores 86% of the known positive instances, while distinguishing them from random matches in 78% of the cases. The conservation score is implemented as a real time application designed to be integrated into other tools. It is currently accessible via a Web Service or through a graphical interface.
conclusionThe conservation score improves the prediction of linear motifs, by discarding those matches that are unlikely to be functional because they have not been conserved during the evolution of the protein sequences. It is especially useful for instances in non-structured regions of the proteins, where a domain masking filtering strategy is not applicable.
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.