AIMC Topic: Proteins

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Computational identification of binding energy hot spots in protein-RNA complexes using an ensemble approach.

Bioinformatics (Oxford, England)
MOTIVATION: Identifying RNA-binding residues, especially energetically favored hot spots, can provide valuable clues for understanding the mechanisms and functional importance of protein-RNA interactions. Yet, limited availability of experimentally r...

Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

Briefings in bioinformatics
Protein secondary structure prediction began in 1951 when Pauling and Corey predicted helical and sheet conformations for protein polypeptide backbone even before the first protein structure was determined. Sixty-five years later, powerful new method...

Post hoc support vector machine learning for impedimetric biosensors based on weak protein-ligand interactions.

The Analyst
Impedimetric biosensors for measuring small molecules based on weak/transient interactions between bioreceptors and target analytes are a challenge for detection electronics, particularly in field studies or in the analysis of complex matrices. Prote...

Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks.

Bioinformatics (Oxford, England)
MOTIVATION: Regulatory sequences are not solely defined by their nucleic acid sequence but also by their relative distances to genomic landmarks such as transcription start site, exon boundaries or polyadenylation site. Deep learning has become the a...

Machine learning accelerates MD-based binding pose prediction between ligands and proteins.

Bioinformatics (Oxford, England)
MOTIVATION: Fast and accurate prediction of protein-ligand binding structures is indispensable for structure-based drug design and accurate estimation of binding free energy of drug candidate molecules in drug discovery. Recently, accurate pose predi...

DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier.

Bioinformatics (Oxford, England)
MOTIVATION: A large number of protein sequences are becoming available through the application of novel high-throughput sequencing technologies. Experimental functional characterization of these proteins is time-consuming and expensive, and is often ...

Structure-based prediction of protein- peptide binding regions using Random Forest.

Bioinformatics (Oxford, England)
MOTIVATION: Protein-peptide interactions are one of the most important biological interactions and play crucial role in many diseases including cancer. Therefore, knowledge of these interactions provides invaluable insights into all cellular processe...

Deep Forest-based Prediction of Protein Subcellular Localization.

Current gene therapy
MOTIVATION: Knowledge of the correct protein subcellular localization is necessary for understanding the function of a protein and revealing the mechanism of many human diseases due to protein subcellular mislocalization, which is required before app...

Perturbation Theory Machine Learning Models: Theory, Regulatory Issues, and Applications to Organic Synthesis, Medicinal Chemistry, Protein Research, and Technology.

Current topics in medicinal chemistry
Machine Learning (ML) models are very useful to predict physicochemical properties of small organic molecules, proteins, proteomes, and complex systems. These methods may be useful to reduce the cost of research in terms of materials resources, time,...

Computing and Visualizing Gene Function Similarity and Coherence with NaviGO.

Methods in molecular biology (Clifton, N.J.)
Gene ontology (GO) is a controlled vocabulary of gene functions across all species, which is widely used for functional analyses of individual genes and large-scale proteomic studies. NaviGO is a webserver for visualizing and quantifying the relation...