Deep learning-based advances in protein structure prediction
Pakhrin, Subash C.
KC, Dukka B.
MetadataShow full item record
Pakhrin, S. C., Shrestha, B., Adhikari, B., & KC, D. B. (2021). Deep learning-based advances in protein structure prediction. International Journal of Molecular Sciences, 22(11) doi:10.3390/ijms22115553
Obtaining an accurate description of protein structure is a fundamental step toward understanding the underpinning of biology. Although recent advances in experimental approaches have greatly enhanced our capabilities to experimentally determine protein structures, the gap between the number of protein sequences and known protein structures is ever increasing. Computational protein structure prediction is one of the ways to fill this gap. Recently, the protein structure prediction field has witnessed a lot of advances due to Deep Learning (DL)-based approaches as evidenced by the success of AlphaFold2 in the most recent Critical Assessment of protein Structure Prediction (CASP14). In this article, we highlight important milestones and progresses in the field of protein structure prediction due to DL-based methods as observed in CASP experiments. We describe advances in various steps of protein structure prediction pipeline viz. protein contact map prediction, protein distogram prediction, protein real-valued distance prediction, and Quality Assessment/refinement. We also highlight some end-to-end DL-based approaches for protein structure prediction approaches. Additionally, as there have been some recent DL-based advances in protein structure determination using Cryo-Electron (Cryo-EM) microscopy based, we also highlight some of the important progress in the field. Finally, we provide an outlook and possible future research directions for DL-based approaches in the protein structure prediction arena.
Showing items related by title, author, creator and subject.
Comparative effects of whey protein versus L-leucine on skeletal muscle protein synthesis and markers of ribosome biogenesis following resistance exercise Mobley, C. Brooks; Fox, Carlton D.; Thompson, Richard M.; Healy, James C.; Santucci, Vincent; Kephart, Wesley C.; McCloskey, Anna E.; Kim, Mike; Pascoe, David D.; Martin, Jeffrey S.; Moon, Jordan R.; Young, Kaelin C.; Roberts, Michael D. (Springer Vienna, 2016-03)We compared immediate post-exercise whey protein (WP, 500 mg) versus l-leucine (LEU, 54 mg) feedings on skeletal muscle protein synthesis (MPS) mechanisms and ribosome biogenesis markers 3 h following unilateral plantarflexor ...
Thompson, Peter M.; Beck, Moriah R.; Campbell, Sharon L. (Springer New York, 2015)Nuclear magnetic resonance (NMR) has continued to evolve as a powerful method, with an increase in the number of pulse sequences and techniques available to study protein-protein interactions. In this chapter, a straightforward ...
Hardware acceleration of the STRIKE string kernel algorithm for estimating protein to protein interactions Sibai, Fadi N.; El-Moursy, Ali A.; Asaduzzaman, Abu; Majzoub, Sohaib S. (IEEE, 2021-03-17)Protein-protein interaction (PPI) is an important field in bioinformatics which helps in understanding diseases and devising therapy. PPI aims at estimating the similarity of protein sequences and their common regions. ...