AIMC Topic: Computational Biology

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Leveraging high-throughput screening data, deep neural networks, and conditional generative adversarial networks to advance predictive toxicology.

PLoS computational biology
There are currently 85,000 chemicals registered with the Environmental Protection Agency (EPA) under the Toxic Substances Control Act, but only a small fraction have measured toxicological data. To address this gap, high-throughput screening (HTS) an...

Identification of subtypes of anticancer peptides based on sequential features and physicochemical properties.

Scientific reports
Anticancer peptides (ACPs) are a kind of bioactive peptides which could be used as a novel type of anticancer drug that has several advantages over chemistry-based drug, including high specificity, strong tumor penetration capacity, and low toxicity ...

Physics-based protein structure refinement in the era of artificial intelligence.

Proteins
Protein structure refinement is the last step in protein structure prediction pipelines. Physics-based refinement via molecular dynamics (MD) simulations has made significant progress during recent years. During CASP14, we tested a new refinement pro...

Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications.

Nature communications
Recent studies suggest that epi-transcriptome regulation via post-transcriptional RNA modifications is vital for all RNA types. Precise identification of RNA modification sites is essential for understanding the functions and regulatory mechanisms of...

Immune-Based Prediction of COVID-19 Severity and Chronicity Decoded Using Machine Learning.

Frontiers in immunology
Expression of CCR5 and its cognate ligands have been implicated in COVID-19 pathogenesis, consequently therapeutics directed against CCR5 are being investigated. Here, we explored the role of CCR5 and its ligands across the immunologic spectrum of CO...

Construction and Validation of a Lung Cancer Diagnostic Model Based on 6-Gene Methylation Frequency in Blood, Clinical Features, and Serum Tumor Markers.

Computational and mathematical methods in medicine
Lung cancer has a high mortality rate. Promoting early diagnosis and screening of lung cancer is the most effective way to enhance the survival rate of lung cancer patients. Through computer technology, a comprehensive evaluation of genetic testing r...

TopDomain: Exhaustive Protein Domain Boundary Metaprediction Combining Multisource Information and Deep Learning.

Journal of chemical theory and computation
Protein domains are independent, functional, and stable structural units of proteins. Accurate protein domain boundary prediction plays an important role in understanding protein structure and evolution, as well as for protein structure prediction. C...

Behavioral correlates of cortical semantic representations modeled by word vectors.

PLoS computational biology
The quantitative modeling of semantic representations in the brain plays a key role in understanding the neural basis of semantic processing. Previous studies have demonstrated that word vectors, which were originally developed for use in the field o...

Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations.

Cell reports methods
Structure prediction for proteins lacking homologous templates in the Protein Data Bank (PDB) remains a significant unsolved problem. We developed a protocol, C-I-TASSER, to integrate interresidue contact maps from deep neural-network learning with t...

A Real-Time Clinical Decision Support System, for Mild Cognitive Impairment Detection, Based on a Hybrid Neural Architecture.

Computational and mathematical methods in medicine
Clinical procedure for mild cognitive impairment (MCI) is mainly based on clinical records and short cognitive tests. However, low suspicion and difficulties in understanding test cut-offs make diagnostic accuracy being low, particularly in primary c...