To make sense of the exploding diversity of machine learning approaches, we introduce a unifying framework that classifies models on the basis of their use of three core data modalities: sequences, structures and functional labels. We discuss the new capabilities and outstanding challenges for the ...
including (1) the effectiveness of graph representations and backbones with native protein structures, (2) the model tolerance with low-quality protein structures, (3) the capability to predict motifs (i.e., functional sites) in a protein, (4) the overall and type-specific feature importance....
S. cerevisiaeis also amongst the most well-annotated genomes, making it ideal for functional analysis using the Gene Ontology [18]. In agreement with previous estimates [36], our LCR-detection method (see Methods) found that of 6, 165S. cerevisiaeproteins documented in UniProt, 1; 306 contai...
This phosphorylation usually results in a functional change of the substrate and is among the most common mechanisms of cell signaling in both eukaryotes and prokaryotes (Walsh and Van Patten, 1994; Smith et al., 1999; Shabb, 2001). Protein kinase A (PKA), also known as cAMP-dependent ...
A bioinformatics pipeline to search functional motifs within whole-proteome data: a case study of poxviruses protein sequences (proteome-wide), (iii) search for motifs containing repeated residues (low-complexity regions, e.g., Leu-, SR-, PEST-rich motifs, ... H Sobhy - 《Virus Genes》 ...
Milk proteins and milk protein-derived peptides have been widely studied for their health enhancing properties. This chapter presents the updated scientific knowledge on the bioactive properties of milk protein-derived peptides. The different bioactive p
We apply CurcAGN to predicting the protein-ligand binding affinity. We train and validate our model on the publicly available standard PDBbind-v2016 dataset, and show that it outperforms SIGN [2] by 7.5% in RMSE and 9.4% in MAE.
Seedorf, U. (1998). Functional Analysis of Sterol Carrier Protein-2 (SCP2) in the SCP2 Knockout Mouse. In: Chang, T.Y., Freeman, D.A. (eds) Intracellular Cholesterol Trafficking. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-5113-3_15 ...
large protein complex is more likely to be able to provide the correct functional groups for catalysis, have the correct complementarity to its substrate, and also be bulky enough to provide a low dielectric environment for its catalytic process if needed43. While large complexes with cyclic or ...
Here, we describe a method based on GCNs for functionally annotating proteins and detecting functional regions in proteins, termed Deep Functional Residue Identification (DeepFRI), that outperforms current methods and scales to the size of current repositories of sequence information. Our model has a...