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ART FounDATion-LOG (ARabidopsis Transcription regulatory Factor Domain-domain interaction Analysis Tool-Liquid liquid phase separation, Oligomerization, Go analysis), a toolkit for interaction data based domain analysis
Kang, J.E.; Jun, J.H.; Kwon, J.H.; Lee, J.-H.; Hwang, K.; Kim, S.; Jeong, N. Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool—Liquid/Liquid Phase Separation, Oligomerization, GO Analysis: A Toolkit for Interaction Data-Based Domain Analysis. Genes2023, 14, 1476.
Kang, J.E.; Jun, J.H.; Kwon, J.H.; Lee, J.-H.; Hwang, K.; Kim, S.; Jeong, N. Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool—Liquid/Liquid Phase Separation, Oligomerization, GO Analysis: A Toolkit for Interaction Data-Based Domain Analysis. Genes 2023, 14, 1476.
Kang, J.E.; Jun, J.H.; Kwon, J.H.; Lee, J.-H.; Hwang, K.; Kim, S.; Jeong, N. Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool—Liquid/Liquid Phase Separation, Oligomerization, GO Analysis: A Toolkit for Interaction Data-Based Domain Analysis. Genes2023, 14, 1476.
Kang, J.E.; Jun, J.H.; Kwon, J.H.; Lee, J.-H.; Hwang, K.; Kim, S.; Jeong, N. Arabidopsis Transcription Regulatory Factor Domain/Domain Interaction Analysis Tool—Liquid/Liquid Phase Separation, Oligomerization, GO Analysis: A Toolkit for Interaction Data-Based Domain Analysis. Genes 2023, 14, 1476.
Abstract
Although there are a large number of databases available for regulatory elements, bottleneck has been created by the lack of bioinformatics tools for predicting types of mechanisms underlying actions of regulatory elements. To reduce the gap, we developed ARabidopsis Transcription regulatory Factor Domain-domain interaction Analysis Tool- Liquid-liquid phase separation (LLPS), Oligomerization, GO analysis (ART FounDATion-LOG), a useful toolkit for protein-nucleic acid interactions (PNI) and protein-protein interactions (PPI) analysis based on domain-domain interaction (DDI). LLPS, protein oligomerization, structural properties of protein domains, and protein modifications are major components in orchestrating spatio-temporal dynamics of PPI and PNI. Our goal is to integrate PPI/PNI information into development of prediction model for identifying important genetic variants in peach. The program unified inter-database relational keys by protein domains for facilitating inference from the model species. Key advantage of the program lies in the integrated information of related features: LOG, structural characterization of domain (e.g. domain linker, intrinsically disordered regions, DDI, domain-motif (peptide) interaction, beta-sheet and transmembrane helices), and post-translational modification. We provided simple tests to demonstrate how to use the program. The program may be applied to other eukaryotic organisms. The program codes and data are freely available for download at and https://sourceforge.net/projects/artfoundation-log/.
Copyright:
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