AIMC Topic: Software

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To Fly, or Not to Fly, That Is the Question: A Deep Learning Model for Peptide Detectability Prediction in Mass Spectrometry.

Journal of proteome research
Identifying detectable peptides, known as flyers, is key in mass spectrometry-based proteomics. Peptide detectability is strongly related to peptide sequences and their resulting physicochemical properties. Moreover, the high variability in MS data c...

MEGA-GPT: Artificial Intelligence Guidance and Building Analytical Protocols Using MEGA Software.

Molecular biology and evolution
Over the past three decades, the Molecular Evolutionary Genetics Analysis (MEGA) software has evolved into a powerful tool with an ever-expanding suite of functionalities. Yet, despite its user-friendly design and widespread adoption by researchers a...

DeepAllo: allosteric site prediction using protein language model (pLM) with multitask learning.

Bioinformatics (Oxford, England)
MOTIVATION: Allostery, the process by which binding at one site perturbs a distant site, is being rendered as a key focus in the field of drug development with its substantial impact on protein function. The identification of allosteric pockets (site...

CrossAttOmics: multiomics data integration with cross-attention.

Bioinformatics (Oxford, England)
MOTIVATION: Advances in high throughput technologies enabled large access to various types of omics. Each omics provides a partial view of the underlying biological process. Integrating multiple omics layers would help have a more accurate diagnosis....

Early outcomes with virtual surgical planning software and patient-specific instrumentation in adult spinal deformity.

Neurosurgical focus
OBJECTIVE: Software engineering innovations have led to the development of virtual surgical planning software (VSPS) for deformity correction. VSPS uses calibrated radiographs and machine learning predictive models to simulate postoperative spinopelv...

DRBP-EDP: classification of DNA-binding proteins and RNA-binding proteins using ESM-2 and dual-path neural network.

NAR genomics and bioinformatics
Regulation of DNA or RNA at the transcriptional, post-transcriptional, and translational levels are key steps in the central dogma of molecular biology. DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs) play pivotal roles in the precise reg...

THERE: Toward an easy and reliable tool for automatic cephalometric analysis.

Computers in biology and medicine
BACKGROUND: Cephalometric analysis in orthodontics is a meticulous process requiring high precision in identifying anatomical landmarks on lateral cephalometric radiographs. Manual analysis by clinicians remains the standard, as even slight deviation...

AITom: AI-guided cryo-electron tomography image analyses toolkit.

Journal of structural biology
Cryo-electron tomography (cryo-ET) is an essential tool in structural biology, uniquely capable of visualizing three-dimensional macromolecular complexes within their native cellular environments, thereby providing profound molecular-level insights. ...

AutoFE-Pointer: Auto-weighted feature extractor based on pointer network for DNA methylation prediction.

International journal of biological macromolecules
DNA methylation is a critical epigenetic modification that plays a central role in gene regulation, cellular differentiation, and the development of various diseases, including cancers. Aberrant methylation patterns have emerged as both biomarkers an...

GOReverseLookup: A gene ontology reverse lookup tool.

Computers in biology and medicine
BACKGROUND AND OBJECTIVE: The Gene Ontology (GO) project has been pivotal in providing a structured framework for characterizing genes and annotating them to specific biological concepts. While traditional gene annotation primarily focuses on mapping...