AIMC Topic: Proteins

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Deep fusion learning facilitates anatomical therapeutic chemical recognition in drug repurposing and discovery.

Briefings in bioinformatics
The advent of large-scale biomedical data and computational algorithms provides new opportunities for drug repurposing and discovery. It is of great interest to find an appropriate data representation and modeling method to facilitate these studies. ...

PScL-HDeep: image-based prediction of protein subcellular location in human tissue using ensemble learning of handcrafted and deep learned features with two-layer feature selection.

Briefings in bioinformatics
Protein subcellular localization plays a crucial role in characterizing the function of proteins and understanding various cellular processes. Therefore, accurate identification of protein subcellular location is an important yet challenging task. Nu...

Improved prediction of protein-protein interaction using a hybrid of functional-link Siamese neural network and gradient boosting machines.

Briefings in bioinformatics
In this paper, for accurate prediction of protein-protein interaction (PPI), a novel hybrid classifier is developed by combining the functional-link Siamese neural network (FSNN) with the light gradient boosting machine (LGBM) classifier. The hybrid ...

Improving protein fold recognition using triplet network and ensemble deep learning.

Briefings in bioinformatics
Protein fold recognition is a critical step toward protein structure and function prediction, aiming at providing the most likely fold type of the query protein. In recent years, the development of deep learning (DL) technique has led to massive adva...

Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins.

Briefings in bioinformatics
Accurate variant effect prediction has broad impacts on protein engineering. Recent machine learning approaches toward this end are based on representation learning, by which feature vectors are learned and generated from unlabeled sequences. However...

Machine learning builds full-QM precision protein force fields in seconds.

Briefings in bioinformatics
Full-quantum mechanics (QM) calculations are extraordinarily precise but difficult to apply to large systems, such as biomolecules. Motivated by the massive demand for efficient calculations for large systems at the full-QM level and by the significa...

Forman persistent Ricci curvature (FPRC)-based machine learning models for protein-ligand binding affinity prediction.

Briefings in bioinformatics
Artificial intelligence (AI) techniques have already been gradually applied to the entire drug design process, from target discovery, lead discovery, lead optimization and preclinical development to the final three phases of clinical trials. Currentl...

Deep Learning Proteins using a Triplet-BERT network.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
Modern sequencing technology has produced a vast quantity of proteomic data, which has been key to the development of various deep learning models within the field. However, there are still challenges to overcome with regards to modelling the propert...

The Impact of Crystallographic Data for the Development of Machine Learning Models to Predict Protein-Ligand Binding Affinity.

Current medicinal chemistry
BACKGROUND: One of the main challenges in the early stages of drug discovery is the computational assessment of protein-ligand binding affinity. Machine learning techniques can contribute to predicting this type of interaction. We may apply these tec...