AIMC Topic: Proteins

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Fold-LTR-TCP: protein fold recognition based on triadic closure principle.

Briefings in bioinformatics
As an important task in protein structure and function studies, protein fold recognition has attracted more and more attention. The existing computational predictors in this field treat this task as a multi-classification problem, ignoring the relati...

MotifCNN-fold: protein fold recognition based on fold-specific features extracted by motif-based convolutional neural networks.

Briefings in bioinformatics
Protein fold recognition is one of the most critical tasks to explore the structures and functions of the proteins based on their primary sequence information. The existing protein fold recognition approaches rely on features reflecting the character...

[3D printed portable gel electrophoresis device for rapid detection of proteins].

Se pu = Chinese journal of chromatography
The growing demand for rapid, portable, and economical detection methods for environmental analysis has resulted in increasing demands on the portability and miniaturization of analytical instruments. The miniaturization of scientific instruments fac...

DeepCDA: deep cross-domain compound-protein affinity prediction through LSTM and convolutional neural networks.

Bioinformatics (Oxford, England)
MOTIVATION: An essential part of drug discovery is the accurate prediction of the binding affinity of new compound-protein pairs. Most of the standard computational methods assume that compounds or proteins of the test data are observed during the tr...

SAINT: self-attention augmented inception-inside-inception network improves protein secondary structure prediction.

Bioinformatics (Oxford, England)
MOTIVATION: Protein structures provide basic insight into how they can interact with other proteins, their functions and biological roles in an organism. Experimental methods (e.g. X-ray crystallography and nuclear magnetic resonance spectroscopy) fo...

UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.

Bioinformatics (Oxford, England)
MOTIVATION: The number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result of genome sequencing and the prediction of protein-coding genes. Providing functional annotation for the...

DeepRMethylSite: a deep learning based approach for prediction of arginine methylation sites in proteins.

Molecular omics
Methylation, which is one of the most prominent post-translational modifications on proteins, regulates many important cellular functions. Though several model-based methylation site predictors have been reported, all existing methods employ machine ...

DeepSVM-fold: protein fold recognition by combining support vector machines and pairwise sequence similarity scores generated by deep learning networks.

Briefings in bioinformatics
Protein fold recognition is critical for studying the structures and functions of proteins. The existing protein fold recognition approaches failed to efficiently calculate the pairwise sequence similarity scores of the proteins in the same fold shar...

Multitask deep networks with grid featurization achieve improved scoring performance for protein-ligand binding.

Chemical biology & drug design
Deep learning-based methods have been extensively developed to improve scoring performance in structure-based drug discovery. Extending multitask deep networks in addressing pharmaceutical problems shows remarkable improvements over single task netwo...

TransformerCPI: improving compound-protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments.

Bioinformatics (Oxford, England)
MOTIVATION: Identifying compound-protein interaction (CPI) is a crucial task in drug discovery and chemogenomics studies, and proteins without three-dimensional structure account for a large part of potential biological targets, which requires develo...