AIMC Topic: Software

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Int&in: A machine learning-based web server for active split site identification in inteins.

Protein science : a publication of the Protein Society
Inteins are proteins that excise themselves out of host proteins and ligate the flanking polypeptides in an auto-catalytic process called protein splicing. In nature, inteins are either contiguous or split. In the case of split inteins, the two fragm...

Clinical evaluation of the efficacy of limbus artificial intelligence software to augment contouring for prostate and nodes radiotherapy.

The British journal of radiology
OBJECTIVES: To determine if Limbus, an artificial intelligence (AI) auto-contouring software, can offer meaningful time savings for prostate radiotherapy treatment planning.

CELA-MFP: a contrast-enhanced and label-adaptive framework for multi-functional therapeutic peptides prediction.

Briefings in bioinformatics
Functional peptides play crucial roles in various biological processes and hold significant potential in many fields such as drug discovery and biotechnology. Accurately predicting the functions of peptides is essential for understanding their divers...

PTFSpot: deep co-learning on transcription factors and their binding regions attains impeccable universality in plants.

Briefings in bioinformatics
Unlike animals, variability in transcription factors (TFs) and their binding regions (TFBRs) across the plants species is a major problem that most of the existing TFBR finding software fail to tackle, rendering them hardly of any use. This limitatio...

Highly accurate classification and discovery of microbial protein-coding gene functions using FunGeneTyper: an extensible deep learning framework.

Briefings in bioinformatics
High-throughput DNA sequencing technologies decode tremendous amounts of microbial protein-coding gene sequences. However, accurately assigning protein functions to novel gene sequences remain a challenge. To this end, we developed FunGeneTyper, an e...

PlasmidHunter: accurate and fast prediction of plasmid sequences using gene content profile and machine learning.

Briefings in bioinformatics
Plasmids are extrachromosomal DNA found in microorganisms. They often carry beneficial genes that help bacteria adapt to harsh conditions. Plasmids are also important tools in genetic engineering, gene therapy, and drug production. However, it can be...

ifDEEPre: large protein language-based deep learning enables interpretable and fast predictions of enzyme commission numbers.

Briefings in bioinformatics
Accurate understanding of the biological functions of enzymes is vital for various tasks in both pathologies and industrial biotechnology. However, the existing methods are usually not fast enough and lack explanations on the prediction results, whic...

MvMRL: a multi-view molecular representation learning method for molecular property prediction.

Briefings in bioinformatics
Effective molecular representation learning is very important for Artificial Intelligence-driven Drug Design because it affects the accuracy and efficiency of molecular property prediction and other molecular modeling relevant tasks. However, previou...

Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning.

Cell systems
Image-based spatial transcriptomics methods enable transcriptome-scale gene expression measurements with spatial information but require complex, manually tuned analysis pipelines. We present Polaris, an analysis pipeline for image-based spatial tran...