AIMC Topic: Computational Biology

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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 ...

Deep-ABPpred: identifying antibacterial peptides in protein sequences using bidirectional LSTM with word2vec.

Briefings in bioinformatics
The overuse of antibiotics has led to emergence of antimicrobial resistance, and as a result, antibacterial peptides (ABPs) are receiving significant attention as an alternative. Identification of effective ABPs in lab from natural sources is a cost-...

NMCMDA: neural multicategory MiRNA-disease association prediction.

Briefings in bioinformatics
MOTIVATION: There is growing evidence showing that the dysregulations of miRNAs cause diseases through various kinds of the underlying mechanism. Thus, predicting the multiple-category associations between microRNAs (miRNAs) and diseases plays an imp...

Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides.

Briefings in bioinformatics
Antimicrobial peptides (AMPs) are a unique and diverse group of molecules that play a crucial role in a myriad of biological processes and cellular functions. AMP-related studies have become increasingly popular in recent years due to antimicrobial r...

SGANRDA: semi-supervised generative adversarial networks for predicting circRNA-disease associations.

Briefings in bioinformatics
Emerging research shows that circular RNA (circRNA) plays a crucial role in the diagnosis, occurrence and prognosis of complex human diseases. Compared with traditional biological experiments, the computational method of fusing multi-source biologica...

PySmash: Python package and individual executable program for representative substructure generation and application.

Briefings in bioinformatics
BACKGROUND: Substructure screening is widely applied to evaluate the molecular potency and ADMET properties of compounds in drug discovery pipelines, and it can also be used to interpret QSAR models for the design of new compounds with desirable phys...

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...

Current status and future perspectives of computational studies on human-virus protein-protein interactions.

Briefings in bioinformatics
The protein-protein interactions (PPIs) between human and viruses mediate viral infection and host immunity processes. Therefore, the study of human-virus PPIs can help us understand the principles of human-virus relationships and can thus guide the ...

Feature extraction approaches for biological sequences: a comparative study of mathematical features.

Briefings in bioinformatics
As consequence of the various genomic sequencing projects, an increasing volume of biological sequence data is being produced. Although machine learning algorithms have been successfully applied to a large number of genomic sequence-related problems,...

A comprehensive overview and critical evaluation of gene regulatory network inference technologies.

Briefings in bioinformatics
Gene regulatory network (GRN) is the important mechanism of maintaining life process, controlling biochemical reaction and regulating compound level, which plays an important role in various organisms and systems. Reconstructing GRN can help us to un...