AIMC Topic: Peptides

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Serum peptide biomarkers by MALDI-TOF MS coupled with machine learning for diagnosis and classification of hepato-pancreato-biliary cancers.

Scientific reports
This study aimed to investigate the potential of peptide mass fingerprints (PMFs) of the serum peptidome using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), in combination with machine learning algorithm...

AAGP integrates physicochemical and compositional features for machine learning-based prediction of anti-aging peptides.

Scientific reports
Aging is a natural phenomenon characterized by the loss of normal morphology and physiological functioning of the body, causing wrinkles on the skin, loss of hair, and compromised immune systems. Peptide therapies have emerged as a promising approach...

Pred5AOP: an efficient screening of food-derived antioxidant peptides based on deep learning, molecular docking, and experimental validation.

Food chemistry
Antioxidant peptides derived from dietary proteins positively impact human health due to their high activity and safety. In this study, a database of 76,343 peptides was constructed via in silico hydrolysis of 29 dietary proteins. A novel antioxidant...

HLAIIPred: cross-attention mechanism for modeling the interaction of HLA class II molecules with peptides.

Communications biology
We introduce HLAIIPred, a deep learning model to predict peptides presented by class II human leukocyte antigens (HLAII) on the surface of antigen presenting cells. HLAIIPred is trained using a Transformer-based neural network and a dataset comprisin...

Integration of pre-trained protein language models with equivariant graph neural networks for peptide toxicity prediction.

BMC biology
BACKGROUND: Peptide-based therapeutics have great potential due to their versatility, high specificity, and suitability for a variety of therapeutic applications. Despite these advantages, the inherent toxicities of some peptides pose challenges in d...

Applications of enhanced sampling methods to biomolecular self-assembly: a review.

Journal of physics. Condensed matter : an Institute of Physics journal
This review article discusses some common enhanced sampling methods in relation to the process of self-assembly of biomolecules. An introduction to self-assembly and its challenges is covered followed by a brief overview of the methods and analysis f...

BPFun: a deep learning framework for bioactive peptide function prediction using multi-label strategy by transformer-driven and sequence rich intrinsic information.

BMC bioinformatics
Bioactive peptides are beneficial or have physiological effects on the life activities of biological organisms. The functions of bioactive peptides are diverse, usually with one or more, so accurately detecting the multiple functions of multi-functio...

MultiRepPI: a cross-modal feature fusion-based multiple characterization framework for plant peptide-protein interaction prediction.

BMC plant biology
Plant peptide-protein interactions (PepPI) play a crucial role in plant growth, development, immune regulation, and environmental adaptation. However, existing computational methods still face several challenges in PepPI prediction. First, most metho...

Evaluation of the False Discovery Rate in Library-Free Search by DIA-NN Using Human Proteome.

Journal of proteome research
Recently, deep-learning-based spectral libraries have gained increasing attention. Several data-independent acquisition (DIA) software tools have integrated this feature, known as a library-free search, thereby making DIA analysis more accessible. H...

Integration of pre-trained GRU and molecular docking for virtual screening of quinoa seed derived ACE inhibitory peptides: An innovative prediction strategy.

Food chemistry
Recent developments in AI, particularly deep learning, are sparking a revolution in bioactive peptide discovery. This study introduced a pretrained Gated Recurrent Unit model (Pre-GRU) to predict the IC values of ACE inhibitory peptides derived from ...