ArticleNAR genomics and bioinformatics2021
LCD-Composer: an intuitive, composition-centric method enabling the identification and detailed functional mapping of low-complexity domains.
Article in NAR genomics and bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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Who cites it
21 citing papers in PubMed.
- How do low-complexity domain interactions control transcription?Biochemical Society transactions · 2026Review
- PERK orchestrates an endoplasmic reticulum stress alternative splicing program via CLK1/SRSF1.Nature communications · 2026Article
- CB-Search: a method for searching for similar protein motifs with biased compositions.BMC bioinformatics · 2026Article
- A composition-matching algorithm, MatchIDR, identifies prion-like domains that localize to stress granules.Protein science : a publication of the Protein Society · 2026Article
- In-Depth Study of Low-Complexity Domains: From Structural Diversity to Disease Mechanisms.Cells · 2025Review
- Article
- Structural Characteristics and Properties of the RNA-Binding Protein hnRNPK at Multiple Physical States.International journal of molecular sciences · 2025Article
- Challenges in adjusting scoring matrices when comparing functional motifs with non-standard compositions.Scientific reports · 2024Article
- LCRAnnotationsDB: a database of low complexity regions functional and structural annotations.BMC genomics · 2024Article
- Identification of Low-Complexity Domains by Compositional Signatures Reveals Class-Specific Frequencies and Functions Across the Domains of Life.PLoS computational biology · 2024Article
- Optimizing strategy for the discovery of compositionally-biased or low-complexity regions in proteins.Scientific reports · 2024Article
- Intrinsically Disordered Compositional Bias in Proteins: Sequence Traits, Region Clustering, and Generation of Hypothetical Functional Associations.Bioinformatics and biology insights · 2024Article
- Protein intrinsically disordered regions have a non-random, modular architecture.Bioinformatics (Oxford, England) · 2023Article
- Article
- The LCD-Composer webserver: high-specificity identification and functional analysis of low-complexity domains in proteins.Bioinformatics (Oxford, England) · 2022Article
- Expansion and functional analysis of the SR-related protein family across the domains of life.RNA (New York, N.Y.) · 2022Article
- Insights from analyses of low complexity regions with canonical methods for protein sequence comparison.Briefings in bioinformatics · 2022Article
- Come together now: Dynamic body-formation of key regulators integrates environmental cues in plant development.Frontiers in plant science · 2022Article
- Regions with two amino acids in protein sequences: A step forward from homorepeats into the low complexity landscape.Computational and structural biotechnology journal · 2022Article
- Generalizable Compositional Features Influencing the Proteostatic Fates of Polar Low-Complexity Domains.International journal of molecular sciences · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Low complexity domains (LCDs) in proteins are regions predominantly composed of a small subset of the possible amino acids. LCDs are involved in a variety of normal and pathological processes across all domains of life. Existing methods define LCDs using information-theoretical complexity thresholds, sequence alignment with repetitive regions, or statistical overrepresentation of amino acids relative to whole-proteome frequencies. While these methods have proven valuable, they are all indirectly quantifying amino acid composition, which is the fundamental and biologically-relevant feature related to protein sequence complexity. Here, we present a new computational tool, LCD-Composer, that directly identifies LCDs based on amino acid composition and linear amino acid dispersion. Using LCD-Composer's default parameters, we identified simple LCDs across all organisms available through UniProt and provide the resulting data in an accessible form as a resource. Furthermore, we describe large-scale differences between organisms from different domains of life and explore organisms with extreme LCD content for different LCD classes. Finally, we illustrate the versatility and specificity achievable with LCD-Composer by identifying diverse classes of LCDs using both simple and multifaceted composition criteria. We demonstrate that the ability to dissect LCDs based on these multifaceted criteria enhances the functional mapping and classification of LCDs.
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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.