AIMC Topic: Proteins

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A spatial-temporal gated attention module for molecular property prediction based on molecular geometry.

Briefings in bioinformatics
MOTIVATION: Geometry-based properties and characteristics of drug molecules play an important role in drug development for virtual screening in computational chemistry. The 3D characteristics of molecules largely determine the properties of the drug ...

A survey on computational models for predicting protein-protein interactions.

Briefings in bioinformatics
Proteins interact with each other to play critical roles in many biological processes in cells. Although promising, laboratory experiments usually suffer from the disadvantages of being time-consuming and labor-intensive. The results obtained are oft...

Accurate prediction of inter-protein residue-residue contacts for homo-oligomeric protein complexes.

Briefings in bioinformatics
Protein-protein interactions play a fundamental role in all cellular processes. Therefore, determining the structure of protein-protein complexes is crucial to understand their molecular mechanisms and develop drugs targeting the protein-protein inte...

Prediction and collection of protein-metabolite interactions.

Briefings in bioinformatics
Interactions between proteins and small molecule metabolites play vital roles in regulating protein functions and controlling various cellular processes. The activities of metabolic enzymes, transcription factors, transporters and membrane receptors ...

Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation.

Briefings in bioinformatics
As an essential task in protein structure and function prediction, protein fold recognition has attracted increasing attention. The majority of the existing machine learning-based protein fold recognition approaches strongly rely on handcrafted featu...

Accurate prediction of multi-label protein subcellular localization through multi-view feature learning with RBRL classifier.

Briefings in bioinformatics
Multi-label proteins can participate in carrier transportation, enzyme catalysis, hormone regulation and other life activities. Meanwhile, they play a key role in the fields of biopharmaceuticals, gene and cell therapy. This article proposes a predic...

An end-to-end heterogeneous graph representation learning-based framework for drug-target interaction prediction.

Briefings in bioinformatics
Accurately identifying potential drug-target interactions (DTIs) is a key step in drug discovery. Although many related experimental studies have been carried out for identifying DTIs in the past few decades, the biological experiment-based DTI ident...

Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening?

Briefings in bioinformatics
Machine-learning (ML)-based scoring functions (MLSFs) have gradually emerged as a promising alternative for protein-ligand binding affinity prediction and structure-based virtual screening. However, clouds of doubts have still been raised against the...

SubLocEP: a novel ensemble predictor of subcellular localization of eukaryotic mRNA based on machine learning.

Briefings in bioinformatics
MOTIVATION: mRNA location corresponds to the location of protein translation and contributes to precise spatial and temporal management of the protein function. However, current assignment of subcellular localization of eukaryotic mRNA reveals import...