A supervised learning framework for chromatin loop detection in genome-wide contact maps
Sign Up to like & getrecommendations! Published in 2020 at "Nature Communications"
DOI: 10.1038/s41467-020-17239-9
Abstract: Accurately predicting chromatin loops from genome-wide interaction matrices such as Hi-C data is critical to deepening our understanding of proper gene regulation. Current approaches are mainly focused on searching for statistically enriched dots on a… read more here.
Keywords: genome wide; chromatin loops; framework; contact maps ... See more keywords
What geometrically constrained models can tell us about real-world protein contact maps
Sign Up to like & getrecommendations! Published in 2023 at "Physical Biology"
DOI: 10.1088/1478-3975/acd543
Abstract: The mechanisms by which a protein’s 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from… read more here.
Keywords: contact maps; amino acid; protein; geometrically constrained ... See more keywords
Using Attention-UNet Models to Predict Protein Contact Maps
Sign Up to like & getrecommendations! Published in 2024 at "Journal of Computational Biology"
DOI: 10.1089/cmb.2023.0102
Abstract: Proteins are essential to life, and understanding their intrinsic roles requires determining their structure. The field of proteomics has opened up new opportunities by applying deep learning algorithms to large databases of solved protein structures.… read more here.
Keywords: contact maps; attention unet; using attention; protein contact ... See more keywords
Automated method to differentiate between native and mirror protein models obtained from contact maps
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DOI: 10.1371/journal.pone.0196993
Abstract: Mirror protein structures are often considered as artifacts in modeling protein structures. However, they may soon become a new branch of biochemistry. Moreover, methods of protein structure reconstruction, based on their residue-residue contact maps, need… read more here.
Keywords: protein; native mirror; class; contact maps ... See more keywords