AIMC Topic: Algorithms

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Machine-learning scoring functions trained on complexes dissimilar to the test set already outperform classical counterparts on a blind benchmark.

Briefings in bioinformatics
The superior performance of machine-learning scoring functions for docking has caused a series of debates on whether it is due to learning knowledge from training data that are similar in some sense to the test data. With a systematically revised met...

Human host status inference from temporal microbiome changes via recurrent neural networks.

Briefings in bioinformatics
With the rapid increase in sequencing data, human host status inference (e.g. healthy or sick) from microbiome data has become an important issue. Existing studies are mostly based on single-point microbiome composition, while it is rare that the hos...

PSSP-MVIRT: peptide secondary structure prediction based on a multi-view deep learning architecture.

Briefings in bioinformatics
The prediction of peptide secondary structures is fundamentally important to reveal the functional mechanisms of peptides with potential applications as therapeutic molecules. In this study, we propose a multi-view deep learning method named Peptide ...

The accurate prediction and characterization of cancerlectin by a combined machine learning and GO analysis.

Briefings in bioinformatics
Cancerlectins, lectins linked to tumor progression, have become the focus of cancer therapy research for their carbohydrate-binding specificity. However, the specific characterization for cancerlectins involved in tumor progression is still unclear. ...

A novel antibacterial peptide recognition algorithm based on BERT.

Briefings in bioinformatics
As the best substitute for antibiotics, antimicrobial peptides (AMPs) have important research significance. Due to the high cost and difficulty of experimental methods for identifying AMPs, more and more researches are focused on using computational ...

WEVar: a novel statistical learning framework for predicting noncoding regulatory variants.

Briefings in bioinformatics
Understanding the functional consequence of noncoding variants is of great interest. Though genome-wide association studies or quantitative trait locus analyses have identified variants associated with traits or molecular phenotypes, most of them are...

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...

A machine learning framework to predict antibiotic resistance traits and yet unknown genes underlying resistance to specific antibiotics in bacterial strains.

Briefings in bioinformatics
Recently, the frequency of observing bacterial strains without known genetic components underlying phenotypic resistance to antibiotics has increased. There are several strains of bacteria lacking known resistance genes; however, they demonstrate res...

Utilizing graph machine learning within drug discovery and development.

Briefings in bioinformatics
Graph machine learning (GML) is receiving growing interest within the pharmaceutical and biotechnology industries for its ability to model biomolecular structures, the functional relationships between them, and integrate multi-omic datasets - amongst...

NeuroPred-FRL: an interpretable prediction model for identifying neuropeptide using feature representation learning.

Briefings in bioinformatics
Neuropeptides (NPs) are the most versatile neurotransmitters in the immune systems that regulate various central anxious hormones. An efficient and effective bioinformatics tool for rapid and accurate large-scale identification of NPs is critical in ...