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Updated: Nov 4, 2025

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
Published on: October 3, 2018
LCD-Composer: an intuitive, composition-centric method enabling the identification and detailed functional mapping of
Sean M Cascarina1, David C King1, Erin Osborne Nishimura1
1Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.
We developed LCD-Composer, a new tool to directly identify protein Low Complexity Domains (LCDs) by analyzing amino acid composition. This method offers a more fundamental approach to understanding protein complexity across all life forms.
Area of Science:
- Biochemistry
- Bioinformatics
- Computational Biology
Background:
- Low Complexity Domains (LCDs) are protein regions with limited amino acid diversity, crucial in biological processes.
- Current methods for LCD identification indirectly assess amino acid composition, limiting direct analysis.
- Understanding LCDs is vital for comprehending protein function and evolution.
Purpose of the Study:
- To introduce LCD-Composer, a novel computational tool for direct identification of LCDs based on amino acid composition and dispersion.
- To provide a comprehensive resource of identified LCDs across diverse organisms.
- To explore inter-organismal variations in LCD content and characteristics.
Main Methods:
- Development of LCD-Composer, a tool utilizing direct amino acid composition and linear dispersion analysis.
- Application of LCD-Composer to identify simple LCDs across all UniProt organisms.
- Analysis of large-scale LCD data to identify inter-domain differences and extreme cases.
Main Results:
- Successful identification of simple LCDs across a wide range of organisms using LCD-Composer.
- Discovery of significant differences in LCD content and types between various domains of life.
- Demonstration of LCD-Composer's capability to identify diverse LCD classes using multifaceted criteria.
Conclusions:
- LCD-Composer provides a direct and versatile method for identifying and classifying protein LCDs.
- The tool enhances functional mapping and classification of LCDs by enabling dissection based on specific composition criteria.
- The generated LCD data serves as a valuable resource for further biological research.
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