AIMC Topic: Computational Biology
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Cyclic peptide structure prediction and design using AlphaFold2.
Nature communications
May 21, 2025
Small cyclic peptides have gained significant traction as a therapeutic modality; however, the development of deep learning methods for accurately designing such peptides has been slow, mostly due to the lack of sufficiently large training sets. Here...
TCoCPIn reveals topological characteristics of chemical protein interaction networks for novel feature discovery.
Scientific reports
May 18, 2025
Understanding chemical-protein interactions (CPIs) is crucial for drug discovery and biological research, yet their complexity often challenges traditional methods. We propose TCoCPIn, a novel framework integrating graph neural networks (GNN) with th...
The underlying molecular mechanisms and biomarkers of Hip fracture combined with deep vein thrombosis based on self sequencing bioinformatics analysis.
Journal of orthopaedic surgery and research
May 16, 2025
BACKGROUND: Thrombus formation is a severe complication in orthopedic surgery, significantly increasing mortality in patients with fractures. Therefore, identifying feature genes to determine thrombus presence in fracture surgeries is critical.
Multi-criteria decision making and its application to in silico discovery of vaccine candidates for Toxoplasma gondii.
Vaccine
May 15, 2025
Vaccine discovery against eukaryotic parasites is not trivial and few exist. Reverse vaccinology is an in silico vaccine discovery approach, designed to identify vaccine candidates from the thousands of protein sequences encoded by a target genome. P...
Exploring potential diagnostic markers and therapeutic targets for type 2 diabetes mellitus with major depressive disorder through bioinformatics and in vivo experiments.
Scientific reports
May 15, 2025
Type 2 diabetes mellitus (T2DM) and Major depressive disorder (MDD) act as risk factors for each other, and the comorbidity of both significantly increases the all-cause mortality rate. Therefore, studying the diagnosis and treatment of diabetes with...
Exon-intron boundary detection made easy by physicochemical properties of DNA.
Molecular omics
May 15, 2025
Genome architecture in eukaryotes exhibits a high degree of complexity. Amidst the numerous intricacies, the existence of genes as non-continuous stretches composed of exons and introns has garnered significant attention and curiosity among researche...
iEnhancer-GDM: A Deep Learning Framework Based on Generative Adversarial Network and Multi-head Attention Mechanism to Identify Enhancers and Their Strength.
Interdisciplinary sciences, computational life sciences
May 7, 2025
Enhancers are short DNA fragments capable of significantly increase the frequency of gene transcription. They often exert their effects on targeted genes over long distances, either in cis or in trans configurations. Identifying enhancers poses a cha...
Learning a deep language model for microbiomes: The power of large scale unlabeled microbiome data.
PLoS computational biology
May 7, 2025
We use open source human gut microbiome data to learn a microbial "language" model by adapting techniques from Natural Language Processing (NLP). Our microbial "language" model is trained in a self-supervised fashion (i.e., without additional externa...
A KAN-based hybrid deep neural networks for accurate identification of transcription factor binding sites.
PloS one
May 7, 2025
BACKGROUND: Predicting protein-DNA binding sites in vivo is a challenging but urgent task in many fields such as drug design and development. Most promoters contain many transcription factor (TF) binding sites, yet only a few have been identified thr...
Structural Biology in the AlphaFold Era: How Far Is Artificial Intelligence from Deciphering the Protein Folding Code?
Biomolecules
May 6, 2025
Proteins are biomolecules characterized by uncommon chemical and physicochemical complexities coupled with extreme responsiveness to even minor chemical modifications or environmental variations. Since the shape that proteins assume is fundamental fo...
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