AIMC Topic: Software

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Computational Ion Channel Research: from the Application of Artificial Intelligence to Molecular Dynamics Simulations.

Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology
Although ion channels are crucial in many physiological processes and constitute an important class of drug targets, much is still unclear about their function and possible malfunctions that lead to diseases. In recent years, computational methods ha...

CRISPRidentify: identification of CRISPR arrays using machine learning approach.

Nucleic acids research
CRISPR-Cas are adaptive immune systems that degrade foreign genetic elements in archaea and bacteria. In carrying out their immune functions, CRISPR-Cas systems heavily rely on RNA components. These CRISPR (cr) RNAs are repeat-spacer units that are p...

The Auto-eFACE: Machine Learning-Enhanced Program Yields Automated Facial Palsy Assessment Tool.

Plastic and reconstructive surgery
BACKGROUND: Facial palsy assessment is nonstandardized. Clinician-graded scales are limited by subjectivity and observer bias. Computer-aided grading would be desirable to achieve conformity in facial palsy assessment and to compare the effectiveness...

ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity.

Bioinformatics (Oxford, England)
MOTIVATION: Genetically engineering food crops involves introducing proteins from other species into crop plant species or modifying already existing proteins with gene editing techniques. In addition, newly synthesized proteins can be used as therap...

A deep learning-based medication behavior monitoring system.

Mathematical biosciences and engineering : MBE
The internet of things (IoT) and deep learning are emerging technologies in diverse research fields, including the provision of IT services in medical domains. In the COVID-19 era, intelligent medication behavior monitoring systems for stable patient...

Lilikoi V2.0: a deep learning-enabled, personalized pathway-based R package for diagnosis and prognosis predictions using metabolomics data.

GigaScience
BACKGROUND: previously we developed Lilikoi, a personalized pathway-based method to classify diseases using metabolomics data. Given the new trends of computation in the metabolomics field, it is important to update Lilikoi software.

The Human Phenotype Ontology in 2021.

Nucleic acids research
The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for ...

Open Targets Platform: supporting systematic drug-target identification and prioritisation.

Nucleic acids research
The Open Targets Platform (https://www.targetvalidation.org/) provides users with a queryable knowledgebase and user interface to aid systematic target identification and prioritisation for drug discovery based upon underlying evidence. It is publicl...

FireProtDB: database of manually curated protein stability data.

Nucleic acids research
The majority of naturally occurring proteins have evolved to function under mild conditions inside the living organisms. One of the critical obstacles for the use of proteins in biotechnological applications is their insufficient stability at elevate...